From 2b9d7267db61b93422be832002cafe504a40e4e2 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 7 Nov 2024 16:09:38 -0800 Subject: [PATCH 1/2] add subject and object specialization qualfiiers to handle MAXO and possibly GO-CAM representations in Biolink --- biolink-model.yaml | 47 +- project/jsonld/biolink_model.context.jsonld | 8 +- project/jsonld/biolink_model.jsonld | 40 +- project/owl/biolink_model.owl.ttl | 5677 +-- project/shacl/biolink_model.shacl.ttl | 43028 +++++++++--------- src/biolink_model/datamodel/model.py | 8 +- src/biolink_model/schema/biolink_model.yaml | 28 + src/biolink_model/scripts/classprefixes.py | 2 +- 8 files changed, 24484 insertions(+), 24354 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index cbfe24ee4..af3f3a5ba 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -1316,6 +1316,26 @@ slots: in_subset: - translator_minimal + specialization qualifier: + is_a: qualifier + abstract: true + description: >- + A qualifier that composes with a core subject/object concept to define a more specific version of the + subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept + and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the + subject identifier. + examples: + - value: CHEBI:5118 # fluoxetine + description: >- + In a MAXO annotation this would be a specialization in treatment of a disease. For example, + fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent + therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term + 'congenital myasthenic syndrome '4A.' + - value: GO:0005634 # nucleus + description: >- + In an expression annotation this would be a specialization in location of an anatomical entity. For example, + "expression in the nucleus of hepatic cells" would be a specialization of "expression in hepatic cells" + aspect qualifier: is_a: qualifier abstract: true @@ -1440,6 +1460,17 @@ slots: in_subset: - translator_minimal + subject specialization qualifier: + is_a: specialization qualifier + description: >- + A qualifier that composes with a core subject/object concept to define a more specific version of the + subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept + and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the + subject identifier. + in_subset: + - translator_minimal + range: uriorcurie + subject form or variant qualifier: description: >- A qualifier that composes with a core subject/object concept to define a specific type, variant, @@ -1506,6 +1537,17 @@ slots: in_subset: - translator_minimal + object specialization qualifier: + is_a: specialization qualifier + description: >- + A qualifier that composes with a core subject/object concept to define a more specific version of the + subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept + and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the + subject identifier. + in_subset: + - translator_minimal + range: uriorcurie + object form or variant qualifier: description: >- A qualifier that composes with a core subject/object concept to define a specific type, variant, @@ -9821,7 +9863,7 @@ classes: chemical or drug or treatment to disease or phenotypic feature association: description: >- This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature - where the disesae or phenotypic feature is a secondary undesirable effect. + where the disease or phenotypic feature is a secondary undesirable effect. is_a: association defining_slots: - subject @@ -10337,6 +10379,9 @@ classes: - object - sex qualifier - disease context qualifier + - subject specialization qualifier + - object specialization qualifier + - anatomical context qualifier defining_slots: - object slot_usage: diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld index d81ced73d..62518fbb8 100644 --- a/project/jsonld/biolink_model.context.jsonld +++ b/project/jsonld/biolink_model.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-10-28T20:58:55", + "generation_date": "2024-11-07T15:54:30", "source": "biolink_model.yaml" }, "@context": { @@ -2166,6 +2166,9 @@ "source_web_page": { "@id": "source_web_page" }, + "specialization_qualifier": { + "@id": "specialization_qualifier" + }, "species_context_qualifier": { "@type": "@id", "@id": "species_context_qualifier" @@ -2257,6 +2260,9 @@ "subject_part_qualifier": { "@id": "subject_part_qualifier" }, + "subject_specialization_qualifier": { + "@id": "subject_specialization_qualifier" + }, "summary": { "@id": "summary" }, diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld index dbfdb39a5..ac4b99bd9 100644 --- a/project/jsonld/biolink_model.jsonld +++ b/project/jsonld/biolink_model.jsonld @@ -3905,6 +3905,31 @@ "range": "string", "@type": "SlotDefinition" }, + { + "name": "specialization_qualifier", + "definition_uri": "https://w3id.org/biolink/vocab/specialization_qualifier", + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "examples": [ + { + "value": "CHEBI:24431", + "description": "In a MAXO annotation this would be a specialization in treatment of a disease. For example, fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term 'congenital myasthenic syndrome '4A.'", + "@type": "Example" + }, + { + "value": "CL:0000123", + "description": "In an expression annotation this would be a specialization in location of an anatomical entity. For example, \"expression in the nucleas of hepatic cells\" would be a specialization of \"expression in hepatic cells\"", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/biolink/biolink-model", + "is_a": "qualifier", + "abstract": true, + "domain": "Association", + "slot_uri": "https://w3id.org/biolink/vocab/specialization_qualifier", + "owner": "specialization_qualifier", + "range": "string", + "@type": "SlotDefinition" + }, { "name": "aspect_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/aspect_qualifier", @@ -4136,6 +4161,15 @@ "range": "string", "@type": "SlotDefinition" }, + { + "name": "subject_specialization_qualifier", + "definition_uri": "https://w3id.org/biolink/vocab/subject_specialization_qualifier", + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "from_schema": "https://w3id.org/biolink/biolink-model", + "slot_uri": "https://w3id.org/biolink/vocab/subject_specialization_qualifier", + "range": "string", + "@type": "SlotDefinition" + }, { "name": "subject_form_or_variant_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_form_or_variant_qualifier", @@ -35761,9 +35795,9 @@ ], "metamodel_version": "1.7.0", "source_file": "biolink_model.yaml", - "source_file_date": "2024-10-28T20:58:52", - "source_file_size": 401272, - "generation_date": "2024-10-28T20:58:57", + "source_file_date": "2024-11-07T15:54:25", + "source_file_size": 402910, + "generation_date": "2024-11-07T15:54:33", "@type": "SchemaDefinition", "@context": [ "project/jsonld/biolink_model.context.jsonld", diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl index 677666ae5..a0cc7ecba 100644 --- a/project/owl/biolink_model.owl.ttl +++ b/project/owl/biolink_model.owl.ttl @@ -1312,6 +1312,12 @@ biolink:severity_qualifier a owl:ObjectProperty ; skos:definition "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; skos:inScheme . +biolink:specialization_qualifier a owl:DatatypeProperty ; + rdfs:label "specialization qualifier" ; + rdfs:subPropertyOf biolink:qualifier ; + skos:definition "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + skos:inScheme . + biolink:start_coordinate a owl:DatatypeProperty ; rdfs:label "start coordinate" ; rdfs:subPropertyOf biolink:base_coordinate ; @@ -1328,6 +1334,11 @@ biolink:subject_location_in_text a owl:DatatypeProperty ; skos:definition "Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion." ; skos:inScheme . +biolink:subject_specialization_qualifier a owl:DatatypeProperty ; + rdfs:label "subject specialization qualifier" ; + skos:definition "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + skos:inScheme . + biolink:superclass_of a owl:ObjectProperty ; rdfs:label "superclass of" ; rdfs:domain biolink:OntologyClass ; @@ -2599,13 +2610,13 @@ biolink:AccessibleDnaRegion a owl:Class ; rdfs:label "accessible dna region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], @@ -2655,15 +2666,21 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -2672,14 +2689,8 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; skos:inScheme . @@ -2690,26 +2701,26 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], @@ -2803,26 +2814,26 @@ biolink:Bacterium a owl:Class ; biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Behavior ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:BehavioralFeature ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; skos:inScheme . @@ -2850,20 +2861,20 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; skos:inScheme . @@ -2889,29 +2900,29 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:label "causal gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3004,8 +3015,11 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -3014,10 +3028,7 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; skos:inScheme . @@ -3031,166 +3042,166 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme . @@ -3198,70 +3209,70 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -3273,106 +3284,106 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_part_qualifier ], biolink:Association ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; skos:exactMatch SIO:001257 ; @@ -3381,20 +3392,20 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment side effect disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; skos:inScheme . @@ -3422,38 +3433,38 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:minCardinality 0 ; + owl:onProperty biolink:catalyst_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:catalyst_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:catalyst_qualifier ], biolink:ChemicalToChemicalAssociation ; skos:definition "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; skos:inScheme . @@ -3461,9 +3472,6 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; @@ -3472,6 +3480,9 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], @@ -3484,25 +3495,25 @@ biolink:ChemicalToPathwayAssociation a owl:Class ; rdfs:label "chemical to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An interaction between a chemical entity and a biological process or pathway." ; skos:exactMatch SIO:001250 ; @@ -3537,10 +3548,10 @@ biolink:ChiSquaredAnalysisResult a owl:Class ; biolink:ClinicalFinding a owl:Class ; rdfs:label "clinical finding" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ClinicalAttribute ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalAttribute ; + owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], biolink:PhenotypicFeature ; skos:definition "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; @@ -3549,10 +3560,10 @@ biolink:ClinicalFinding a owl:Class ; biolink:ClinicalMeasurement a owl:Class ; rdfs:label "clinical measurement" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -3618,38 +3629,38 @@ biolink:ConfidenceLevel a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; owl:allValuesFrom biolink:InformationContentEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 0 ; owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; skos:inScheme . @@ -3657,28 +3668,28 @@ biolink:ContributorAssociation a owl:Class ; biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; rdfs:label "correlated gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3697,10 +3708,10 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; rdfs:label "disease or phenotypic feature exposure" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:PathologicalEntityMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin ], + owl:someValuesFrom biolink:ExposureEvent ], biolink:Attribute ; skos:definition "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; skos:inScheme . @@ -3708,26 +3719,26 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneticInheritance ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneticInheritance ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; skos:inScheme . @@ -3738,10 +3749,10 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; @@ -3754,10 +3765,10 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; rdfs:label "disease to exposure event association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ], + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between an exposure event and a disease." ; skos:inScheme . @@ -3765,41 +3776,41 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Onset ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:FrequencyQuantifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:closeMatch dcid:DiseaseSymptomAssociation ; skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; @@ -3853,15 +3864,15 @@ biolink:DrugToGeneAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a drug and a gene or gene product." ; skos:inScheme ; @@ -3899,58 +3910,58 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; + owl:onProperty biolink:has_evidence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_evidence ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; - owl:onProperty biolink:has_evidence ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:max_research_phase ], + owl:maxCardinality 1 ; + owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_approval_status ], + owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:ResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; - owl:onProperty biolink:clinical_approval_status ], biolink:Association ; skos:inScheme . @@ -3981,10 +3992,10 @@ biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:clinical_approval_status ], biolink:Association ; skos:inScheme . @@ -4026,23 +4037,23 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Exon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Exon ; + owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" ; skos:inScheme . @@ -4050,26 +4061,26 @@ biolink:ExonToTranscriptRelationship a owl:Class ; biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], + owl:minCardinality 0 ; + owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:time ; owl:onProperty biolink:temporal_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:temporal_context_qualifier ], + owl:onProperty biolink:population_context_qualifier ], biolink:Association ; skos:definition "An association between an exposure event and an outcome." ; skos:inScheme . @@ -4077,10 +4088,10 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ExposureEvent ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -4144,176 +4155,176 @@ biolink:Fungus a owl:Class ; biolink:GeneAffectsChemicalAssociation a owl:Class ; rdfs:label "gene affects chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], biolink:Association ; skos:definition "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; skos:inScheme . @@ -4321,31 +4332,34 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "gene as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -4359,23 +4373,20 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -4662,68 +4673,68 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; biolink:GeneRegulatesGeneAssociation a owl:Class ; rdfs:label "gene regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . @@ -4732,49 +4743,49 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; @@ -4784,16 +4795,16 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; @@ -4802,65 +4813,65 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneFamily ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneFamily ; - owl:onProperty biolink:object ], - biolink:Association ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + biolink:Association ; skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; skos:inScheme . biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; skos:inScheme . @@ -4868,32 +4879,32 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneProductMixin ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; skos:inScheme . @@ -4903,6 +4914,9 @@ biolink:GeneToGoTermAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], @@ -4912,9 +4926,6 @@ biolink:GeneToGoTermAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -4926,26 +4937,26 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], biolink:Association ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; skos:inScheme . @@ -4953,29 +4964,29 @@ biolink:GeneToPathwayAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:PhenotypicFeature ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:exactMatch WBVocab:Gene-Phenotype-Association ; skos:inScheme . @@ -4984,13 +4995,13 @@ biolink:Genome a owl:Class ; rdfs:label "genome" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:closeMatch dcid:GenomeAssemblyUnit ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; @@ -5006,19 +5017,19 @@ biolink:GenomicBackgroundExposure a owl:Class ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:ExposureEvent ], biolink:Attribute ; skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; skos:inScheme . @@ -5026,52 +5037,52 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:GenotypeToDiseaseAssociation ; skos:inScheme . biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; skos:inScheme . @@ -5079,32 +5090,32 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ; skos:inScheme . @@ -5114,21 +5125,21 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], @@ -5143,31 +5154,31 @@ biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." ; skos:inScheme . @@ -5206,13 +5217,13 @@ biolink:GeographicExposure a owl:Class ; biolink:GeographicLocationAtTime a owl:Class ; rdfs:label "geographic location at time" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; + owl:maxCardinality 1 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:time ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], biolink:GeographicLocation ; skos:definition "a location that can be described in lat/long coordinates, for a particular time" ; @@ -5237,10 +5248,10 @@ biolink:Haplotype a owl:Class ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:definition "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; skos:exactMatch , @@ -5271,14 +5282,8 @@ biolink:Human a owl:Class ; biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -5287,16 +5292,22 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; skos:inScheme . @@ -5375,6 +5386,9 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:label "macromolecular machine to biological process association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; @@ -5383,9 +5397,6 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; skos:inScheme . @@ -5393,8 +5404,8 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; rdfs:label "macromolecular machine to cellular component association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -5402,8 +5413,8 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; owl:allValuesFrom biolink:CellularComponent ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; skos:inScheme . @@ -5414,14 +5425,14 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; skos:inScheme . @@ -5429,32 +5440,32 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MaterialSample ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." ; skos:inScheme . @@ -5463,10 +5474,10 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "material sample to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "An association between a material sample and a disease or phenotype." ; skos:inScheme . @@ -5489,21 +5500,21 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; @@ -5512,23 +5523,23 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; skos:inScheme . @@ -5537,31 +5548,31 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; skos:inScheme . @@ -5569,77 +5580,77 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . @@ -5654,13 +5665,13 @@ biolink:NucleosomeModification a owl:Class ; rdfs:label "nucleosome modification" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneProductIsoformMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:EpigenomicEntity ], biolink:BiologicalEntity ; skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; skos:inScheme . @@ -5674,64 +5685,58 @@ biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -5739,11 +5744,17 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:associated_environmental_context ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:associated_environmental_context ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; skos:inScheme . @@ -5752,30 +5763,30 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; @@ -5784,29 +5795,35 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismalEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; @@ -5815,62 +5832,56 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:interacting_molecules_category ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 0 ; owl:onProperty biolink:interacting_molecules_category ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:interacting_molecules_category ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; skos:inScheme . @@ -5962,20 +5973,20 @@ biolink:Phenomenon a owl:Class ; biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; rdfs:label "phenotypic feature to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], biolink:Association ; skos:inScheme . @@ -6043,22 +6054,22 @@ biolink:PopulationToPopulationAssociation a owl:Class ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a two populations" ; skos:inScheme . @@ -6075,194 +6086,194 @@ biolink:PosttranslationalModification a owl:Class ; biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:narrow_match ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:mapped_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:narrow_match ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:exact_match ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:narrow_match ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:broad_match ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:mapped_predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:exact_match ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_derivative_qualifier ], linkml:ClassDefinition ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; skos:inScheme . @@ -6278,32 +6289,32 @@ biolink:PreprintPublication a owl:Class ; biolink:ProcessRegulatesProcessAssociation a owl:Class ; rdfs:label "process regulates process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalProcess ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . @@ -6334,10 +6345,10 @@ biolink:ProteinFamily a owl:Class ; rdfs:label "protein family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:BiologicalEntity ; skos:exactMatch , WIKIDATA:Q2278983 ; @@ -6398,13 +6409,13 @@ biolink:RNAProductIsoform a owl:Class ; biolink:ReactionToCatalystAssociation a owl:Class ; rdfs:label "reaction to catalyst association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:ReactionToParticipantAssociation ; skos:inScheme . @@ -6413,10 +6424,10 @@ biolink:ReagentTargetedGene a owl:Class ; rdfs:label "reagent targeted gene" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], @@ -6497,22 +6508,22 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Treatment ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:inScheme ; @@ -6521,47 +6532,47 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], + owl:maxCardinality 1 ; + owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:onProperty biolink:issue ], biolink:Publication ; skos:altLabel "journal" ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; @@ -6610,14 +6621,14 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:allValuesFrom biolink:SocioeconomicAttribute ; + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SocioeconomicAttribute ; - owl:onProperty biolink:has_attribute ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent ], biolink:Attribute ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; skos:inScheme . @@ -6659,22 +6670,22 @@ biolink:StudyVariable a owl:Class ; biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . @@ -6695,20 +6706,20 @@ biolink:TextMiningResult a owl:Class ; biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Transcript ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Transcript ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -6720,16 +6731,16 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; rdfs:label "transcription factor binding site" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:RegulatoryRegion ; skos:altLabel "binding site", "tf binding site" ; @@ -6743,13 +6754,13 @@ biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -6760,17 +6771,17 @@ biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneExpressionMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin ], biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" ; skos:inScheme . @@ -6778,79 +6789,79 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:inScheme . biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], + owl:someValuesFrom biolink:FrequencyQualifierMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_count ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ; skos:inScheme . @@ -7409,41 +7420,41 @@ biolink:AdministrativeEntity a owl:Class ; biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:maxCardinality 1 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:published_in ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:minCardinality 1 ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:issue ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; skos:exactMatch fabio:article, @@ -7454,10 +7465,10 @@ biolink:Behavior a owl:Class ; rdfs:label "behavior" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ActivityAndBehavior ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior ], + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalProcess ; skos:exactMatch STY:T053, ; @@ -7477,31 +7488,31 @@ biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:chapter ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:chapter ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 1 ; owl:onProperty biolink:published_in ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:published_in ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:chapter ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:volume ], biolink:Publication ; skos:inScheme . @@ -7522,17 +7533,17 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], biolink:Association ; skos:definition "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; skos:inScheme . @@ -7569,32 +7580,32 @@ biolink:ChemicalExposure a owl:Class ; biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:FDA_adverse_event_level ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; - owl:onProperty biolink:FDA_adverse_event_level ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:FDA_adverse_event_level ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - biolink:Association ; - skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; - skos:inScheme . + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:FDA_adverse_event_level ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; + owl:onProperty biolink:FDA_adverse_event_level ], + biolink:Association ; + skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; + skos:inScheme . a owl:Class ; rdfs:label "polymorphic_form" ; @@ -7708,10 +7719,10 @@ biolink:GeneFamily a owl:Class ; rdfs:label "gene family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:BiologicalEntity ; skos:altLabel "orthogroup", "protein family" ; @@ -7726,77 +7737,77 @@ biolink:GeneFamily a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:genome_build ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:start_interbase_coordinate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:strand ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhaseEnum ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:phase ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhaseEnum ; - owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:genome_build ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:phase ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:genome_build ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:phase ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -7806,38 +7817,38 @@ biolink:GenomicSequenceLocalization a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7854,18 +7865,18 @@ biolink:GeographicLocation a owl:Class ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:float ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:latitude ], + owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:latitude ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; + owl:maxCardinality 1 ; owl:onProperty biolink:latitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; @@ -7933,10 +7944,10 @@ biolink:Polypeptide a owl:Class ; rdfs:label "polypeptide" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], biolink:BiologicalEntity ; skos:altLabel "amino acid entity" ; skos:definition "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; @@ -7949,37 +7960,37 @@ biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:integer ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:reaction_direction ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:allValuesFrom biolink:ReactionDirectionEnum ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:stoichiometry ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:ReactionSideEnum ; owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stoichiometry ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:reaction_side ], @@ -8015,28 +8026,28 @@ biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_drug ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Device ; owl:onProperty biolink:has_device ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_device ], + owl:allValuesFrom biolink:Procedure ; + owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Procedure ; - owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_procedure ], + owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_procedure ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Device ; + owl:onProperty biolink:has_device ], biolink:NamedThing ; skos:altLabel "medical action", "medical intervention" ; @@ -8049,20 +8060,14 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], @@ -8070,14 +8075,20 @@ biolink:VariantToDiseaseAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], @@ -8088,26 +8099,26 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; skos:inScheme . @@ -8779,23 +8790,23 @@ biolink:ActivityAndBehavior a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -8827,35 +8838,35 @@ biolink:ChemicalRole a owl:Class ; biolink:ChemicalToChemicalAssociation a owl:Class ; rdfs:label "chemical to chemical association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; skos:inScheme . @@ -8932,26 +8943,20 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], @@ -8959,20 +8964,23 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], @@ -8980,7 +8988,10 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:inScheme ; @@ -9041,22 +9052,22 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], biolink:Association ; skos:definition "A relationship between two organism taxon nodes" ; skos:inScheme . @@ -9104,10 +9115,10 @@ biolink:RegulatoryRegion a owl:Class ; rdfs:label "regulatory region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], @@ -9467,10 +9478,10 @@ biolink:DatasetDistribution a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:distribution_download_url ], biolink:InformationContentEntity ; skos:definition "an item that holds distribution level information about a dataset." ; @@ -9481,22 +9492,22 @@ biolink:DatasetSummary a owl:Class ; rdfs:label "dataset summary" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:source_web_page ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:source_logo ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_web_page ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:source_web_page ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:source_logo ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." ; skos:inScheme . @@ -9523,20 +9534,20 @@ biolink:GeneProductIsoformMixin a owl:Class ; biolink:GeneToGeneAssociation a owl:Class ; rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], @@ -9621,23 +9632,23 @@ biolink:Protein a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_numeric_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; - owl:allValuesFrom ; + owl:minCardinality 0 ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_numeric_value ], + owl:onProperty biolink:has_unit ], [ a owl:Restriction ; owl:allValuesFrom xsd:double ; owl:onProperty biolink:has_numeric_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_unit ], + owl:onProperty biolink:has_numeric_value ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; skos:inScheme . @@ -9657,18 +9668,18 @@ biolink:SequenceFeatureRelationship a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; skos:exactMatch CHADO:feature_relationship ; @@ -9789,32 +9800,32 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_distribution ], + owl:allValuesFrom biolink:Dataset ; + owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Dataset ; owl:onProperty biolink:has_dataset ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DatasetDistribution ; + owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:ingest_date ], + owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_distribution ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DatasetDistribution ; + owl:minCardinality 0 ; owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_dataset ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_dataset ], + owl:onProperty biolink:ingest_date ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:ingest_date ], biolink:InformationContentEntity ; skos:definition "an item that holds version level information about a dataset." ; skos:inScheme . @@ -9843,22 +9854,22 @@ biolink:FDAIDAAdverseEventEnum a owl:Class ; biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; @@ -10258,38 +10269,38 @@ biolink:CellularOrganism a owl:Class ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:is_supplement ], + owl:maxCardinality 1 ; + owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], + owl:allValuesFrom biolink:ApprovalStatusEnum ; + owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:allValuesFrom biolink:ApprovalStatusEnum ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], + owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:routes_of_delivery ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; - owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; + owl:onProperty biolink:routes_of_delivery ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:routes_of_delivery ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -10315,28 +10326,28 @@ biolink:GeneProductMixin a owl:Class ; biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:closeMatch dcid:DiseaseGeneAssociation ; @@ -10353,38 +10364,38 @@ biolink:MacromolecularMachineMixin a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:enabled_by ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_output ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_output ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], + owl:onProperty biolink:has_output ], biolink:BiologicalProcessOrActivity ; skos:altLabel "molecular event", "molecular function", @@ -10404,38 +10415,38 @@ biolink:PhysicalEssenceOrOccurrent a owl:Class ; biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_role ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:upstream_resource_ids ], + owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:resource_role ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:resource_id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:resource_id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_id ], + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:allValuesFrom biolink:ResourceRoleEnum ; owl:onProperty biolink:resource_role ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:resource_id ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:resource_id ], + owl:minCardinality 1 ; + owl:onProperty biolink:resource_role ], biolink:InformationContentEntity ; skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; skos:inScheme . @@ -10768,10 +10779,10 @@ biolink:Drug a owl:Class ; rdfs:label "drug" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:OntologyClass ], biolink:MolecularMixture ; skos:broadMatch STY:T121 ; skos:definition "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; @@ -10786,23 +10797,23 @@ biolink:Drug a owl:Class ; biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_zygosity ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Zygosity ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_zygosity ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_zygosity ], biolink:BiologicalEntity ; skos:definition "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; skos:exactMatch , @@ -10898,66 +10909,66 @@ biolink:Entity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:description ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; + owl:minCardinality 0 ; owl:onProperty biolink:deprecated ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:description ], + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_attribute ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom biolink:Attribute ; owl:onProperty biolink:has_attribute ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:deprecated ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], linkml:ClassDefinition ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; skos:inScheme . @@ -11062,12 +11073,12 @@ biolink:OrganismalEntity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:SubjectOfInvestigation ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_attribute ], biolink:BiologicalEntity ; skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; skos:exactMatch , @@ -11152,38 +11163,38 @@ biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhysicalEntity ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:PhysicalEntity ; owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], biolink:BiologicalEntity ; skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; skos:inScheme . @@ -11192,10 +11203,10 @@ biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:onProperty biolink:address ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:affiliation ], + owl:minCardinality 0 ; + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:name ], @@ -11203,25 +11214,25 @@ biolink:Agent a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:address ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:affiliation ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:address ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:address ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:name ], biolink:AdministrativeEntity ; skos:altLabel "group" ; @@ -11309,12 +11320,6 @@ biolink:Occurrent a owl:Class ; skos:exactMatch ; skos:inScheme . -biolink:qualifier a owl:DatatypeProperty ; - rdfs:label "qualifier" ; - rdfs:subPropertyOf biolink:association_slot ; - skos:definition "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - skos:inScheme . - biolink:ExposureEvent a owl:Class ; rdfs:label "exposure event" ; rdfs:subClassOf biolink:OntologyClass ; @@ -11331,6 +11336,12 @@ biolink:qualified_predicate a owl:DatatypeProperty ; skos:editorialNote "to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but does not make sense in the full statement reading (because “Chemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y)" ; skos:inScheme . +biolink:qualifier a owl:DatatypeProperty ; + rdfs:label "qualifier" ; + rdfs:subPropertyOf biolink:association_slot ; + skos:definition "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + skos:inScheme . + biolink:ApprovalStatusEnum a owl:Class ; rdfs:subClassOf linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -11361,13 +11372,13 @@ biolink:DirectionQualifierEnum a owl:Class ; biolink:MolecularEntity a owl:Class ; rdfs:label "molecular entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:is_metabolite ], biolink:ChemicalEntity ; skos:definition "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; @@ -11380,14 +11391,14 @@ biolink:MolecularEntity a owl:Class ; biolink:OrganismTaxon a owl:Class ; rdfs:label "organism taxon" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_taxonomic_rank ], - [ a owl:Restriction ; owl:allValuesFrom biolink:TaxonomicRank ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_taxonomic_rank ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_taxonomic_rank ], biolink:NamedThing ; skos:altLabel "taxon", "taxonomic classification" ; @@ -11402,10 +11413,10 @@ biolink:BiologicalProcess a owl:Class ; rdfs:label "biological process" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:Occurrent ], biolink:BiologicalProcessOrActivity ; skos:broadMatch WIKIDATA:P682 ; skos:definition "One or more causally connected executions of molecular functions" ; @@ -11417,40 +11428,40 @@ biolink:BiologicalProcess a owl:Class ; biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:format ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:license ], + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:format ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:rights ], + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:rights ], + owl:onProperty biolink:format ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:license ], + owl:onProperty biolink:rights ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:license ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:format ], + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:allValuesFrom xsd:date ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:creation_date ], + owl:onProperty biolink:rights ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:rights ], biolink:NamedThing ; skos:altLabel "information", @@ -11509,14 +11520,20 @@ biolink:CausalMechanismQualifierEnum a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quantitative_value ], + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_qualitative_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iri ], @@ -11524,35 +11541,29 @@ biolink:Attribute a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_qualitative_value ], + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 0 ; owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iri ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:allValuesFrom biolink:QuantityValue ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], biolink:NamedThing ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; skos:exactMatch SIO:000614 ; @@ -11577,35 +11588,35 @@ biolink:object_direction_qualifier a owl:ObjectProperty ; biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:symbol ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:symbol ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneOrGeneProduct ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:BiologicalEntity ; skos:broadMatch ; skos:definition "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; @@ -11619,38 +11630,38 @@ biolink:Gene a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_gene ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], biolink:BiologicalEntity ; skos:altLabel "allele" ; skos:closeMatch , @@ -11694,68 +11705,68 @@ biolink:AnatomicalEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:summary ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:publication_type ], + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:authors ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:pages ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; + owl:onProperty biolink:authors ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:keywords ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:mesh_terms ], + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:pages ], + owl:onProperty biolink:publication_type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:keywords ], + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:authors ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:summary ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:publication_type ], + owl:onProperty biolink:keywords ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:mesh_terms ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], biolink:InformationContentEntity ; skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; skos:exactMatch IAO:0000311 ; @@ -11779,17 +11790,32 @@ biolink:BiologicalEntity a owl:Class ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:max_tolerated_dose ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_chemical_role ], + owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_toxic ], @@ -11798,37 +11824,22 @@ biolink:ChemicalEntity a owl:Class ; owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalRole ; - owl:onProperty biolink:has_chemical_role ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:max_tolerated_dose ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:max_tolerated_dose ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:trade_name ], + owl:allValuesFrom biolink:ChemicalRole ; + owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:available_from ], + owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:is_toxic ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], biolink:NamedThing ; skos:broadMatch STY:T167 ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -11967,260 +11978,260 @@ biolink:association_slot a owl:DatatypeProperty ; biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_closure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:KnowledgeLevelEnum ; + owl:onProperty biolink:knowledge_level ], + [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:p_value ], + owl:maxCardinality 1 ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category_closure ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_closure ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:aggregator_knowledge_source ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:primary_knowledge_source ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:primary_knowledge_source ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:agent_type ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; + owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:original_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_object ], + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_namespace ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:AgentTypeEnum ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:original_subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_closure ], + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:primary_knowledge_source ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:original_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_category ], + owl:minCardinality 0 ; + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_predicate ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_predicate ], + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:p_value ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_closure ], + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Study ; - owl:onProperty biolink:has_supporting_studies ], + owl:minCardinality 0 ; + owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_label_closure ], + owl:onProperty biolink:original_object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifier ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Study ; + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_namespace ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:negated ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_namespace ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:original_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:knowledge_source ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_category_closure ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_label_closure ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:negated ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_closure ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_supporting_studies ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:KnowledgeLevelEnum ; + owl:minCardinality 1 ; owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_label_closure ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AgentTypeEnum ; - owl:onProperty biolink:agent_type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_label_closure ], + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:publications ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -12244,25 +12255,19 @@ biolink:NamedThing a owl:Class ; owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:full_name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:provided_by ], + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:synonym ], @@ -12271,7 +12276,13 @@ biolink:NamedThing a owl:Class ; owl:onProperty biolink:provided_by ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:category ], + owl:onProperty biolink:provided_by ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:full_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:synonym ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; skos:exactMatch STY:T071, @@ -12324,72 +12335,42 @@ biolink:subject a owl:ObjectProperty ; skos:inScheme . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocationAtTime ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocationAtTime . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Plant ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Plant . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + rdfs:subClassOf biolink:GeographicLocation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + owl:someValuesFrom biolink:GeographicLocation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptToGeneRelationship ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptToGeneRelationship . + owl:someValuesFrom biolink:Occurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeature ; + rdfs:subClassOf biolink:Serial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeature . + owl:someValuesFrom biolink:Serial . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneAssociation ; + rdfs:subClassOf biolink:ClinicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneAssociation . + owl:someValuesFrom biolink:ClinicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:StudyPopulation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . + owl:someValuesFrom biolink:StudyPopulation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntity ; + rdfs:subClassOf biolink:NamedThing ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntity . + owl:someValuesFrom biolink:NamedThing . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AccessibleDnaRegion ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AccessibleDnaRegion . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SpecificityQuantifier . [] a owl:Restriction ; rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; @@ -12397,505 +12378,338 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:NucleicAcidSequenceMotif . [] a owl:Restriction ; - rdfs:subClassOf biolink:LifeStage ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LifeStage . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Exon ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Exon . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Food ; + rdfs:subClassOf biolink:DatasetSummary ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Food . + owl:someValuesFrom biolink:DatasetSummary . [] a owl:Restriction ; - rdfs:subClassOf biolink:Attribute ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Attribute . + owl:someValuesFrom biolink:GeneToDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . + owl:someValuesFrom biolink:GeneExpressionMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSample ; + rdfs:subClassOf biolink:ChemicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSample . + owl:someValuesFrom biolink:ChemicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Dataset ; + rdfs:subClassOf biolink:ComplexMolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Dataset . + owl:someValuesFrom biolink:ComplexMolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; + rdfs:subClassOf biolink:SocioeconomicAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . + owl:someValuesFrom biolink:SocioeconomicAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGeneAssociation ; + rdfs:subClassOf biolink:MolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGeneAssociation . + owl:someValuesFrom biolink:MolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalFinding ; + rdfs:subClassOf biolink:CellularComponent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalFinding . + owl:someValuesFrom biolink:CellularComponent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Hospitalization ; + rdfs:subClassOf biolink:Genotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Hospitalization . + owl:someValuesFrom biolink:Genotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + rdfs:subClassOf biolink:SocioeconomicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + owl:someValuesFrom biolink:SocioeconomicExposure . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineMixin . + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Case ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin . + rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToGeneProductRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; + rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + rdfs:subClassOf biolink:BioticExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismToOrganismAssociation . + owl:someValuesFrom biolink:BioticExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalMeasurement ; + rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalMeasurement . + owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalModifier ; + rdfs:subClassOf biolink:CellLine ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalModifier . + owl:someValuesFrom biolink:CellLine . [] a owl:Restriction ; - rdfs:subClassOf biolink:Polypeptide ; + rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Polypeptide . + owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . + rdfs:subClassOf biolink:Plant ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Plant . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_quotient ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier . + rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + rdfs:subClassOf biolink:OrganismTaxon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToPathwayAssociation . + owl:someValuesFrom biolink:OrganismTaxon . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass . + owl:someValuesFrom biolink:PathologicalEntityMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularOrganism ; + rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularOrganism . + owl:someValuesFrom biolink:PathologicalAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; + rdfs:subClassOf biolink:DiagnosticAid ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . + owl:someValuesFrom biolink:DiagnosticAid . [] a owl:Restriction ; - rdfs:subClassOf biolink:MicroRNA ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MicroRNA . + owl:someValuesFrom biolink:GeneToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicSex ; + rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicSex . + owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ReactionToCatalystAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin . + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + rdfs:subClassOf biolink:Food ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . + owl:someValuesFrom biolink:Food . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; + rdfs:subClassOf biolink:Vertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . + owl:someValuesFrom biolink:Vertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; + rdfs:subClassOf biolink:PhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneAssociation . + owl:someValuesFrom biolink:PhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetSummary ; + rdfs:subClassOf biolink:Onset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetSummary . + owl:someValuesFrom biolink:Onset . [] a owl:Restriction ; - rdfs:subClassOf biolink:Phenomenon ; + rdfs:subClassOf biolink:Procedure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Phenomenon . + owl:someValuesFrom biolink:Procedure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cohort ; + rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cohort . + owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneProductRelationship . + owl:someValuesFrom biolink:PathologicalAnatomicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Serial ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Serial . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPopulationAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPopulationAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene_or_gene_product ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Human ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Human . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:Procedure ; + rdfs:subClassOf biolink:NucleicAcidEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Procedure . + owl:someValuesFrom biolink:NucleicAcidEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalExposure ; + rdfs:subClassOf biolink:DatasetVersion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalExposure . + owl:someValuesFrom biolink:DatasetVersion . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Haplotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Haplotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:DatasetDistribution ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . + owl:someValuesFrom biolink:DatasetDistribution . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Publication ; + rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Publication . + owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleosomeModification ; + rdfs:subClassOf biolink:BookChapter ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleosomeModification . + owl:someValuesFrom biolink:BookChapter . [] a owl:Restriction ; - rdfs:subClassOf biolink:Case ; + rdfs:subClassOf biolink:ChemicalRole ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Case . + owl:someValuesFrom biolink:ChemicalRole . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Outcome ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalIntervention ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalIntervention . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalMixture ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalMixture . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -12903,108 +12717,127 @@ biolink:subject a owl:ObjectProperty ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceFeatureRelationship . + owl:someValuesFrom biolink:DrugToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Bacterium ; + rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Bacterium . + owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalProcess ; + rdfs:subClassOf biolink:TaxonToTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalProcess . + owl:someValuesFrom biolink:TaxonToTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:RetrievalSource ; + rdfs:subClassOf biolink:Protein ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RetrievalSource . + owl:someValuesFrom biolink:Protein . [] a owl:Restriction ; - rdfs:subClassOf biolink:SeverityValue ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SeverityValue . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:VariantToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:VariantToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AdministrativeEntity ; + rdfs:subClassOf biolink:Human ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AdministrativeEntity . + owl:someValuesFrom biolink:Human . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcessExposure ; + rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcessExposure . + owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Outcome . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DrugExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGoTermAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGoTermAssociation . + owl:someValuesFrom biolink:GeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; + rdfs:subClassOf biolink:EnvironmentalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + owl:someValuesFrom biolink:EnvironmentalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; + rdfs:subClassOf biolink:RNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . + owl:someValuesFrom biolink:RNAProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:Invertebrate ; + rdfs:subClassOf biolink:IndividualOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Invertebrate . + owl:someValuesFrom biolink:IndividualOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genome ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genome . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralExposure . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:disease_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:disease_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:disease_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; @@ -13012,312 +12845,309 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToVariantAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToVariantAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Zygosity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Zygosity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Agent ; + rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Agent . + owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BioticExposure ; + rdfs:subClassOf biolink:ClinicalCourse ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BioticExposure . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathognomonicityQuantifier . + owl:someValuesFrom biolink:ClinicalCourse . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + rdfs:subClassOf biolink:ReagentTargetedGene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + owl:someValuesFrom biolink:ReagentTargetedGene . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; + rdfs:subClassOf biolink:Transcript ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + owl:someValuesFrom biolink:Transcript . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty biolink:has_gene_or_gene_product ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity . + owl:someValuesFrom biolink:GeneGroupingMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntity ; + rdfs:subClassOf biolink:SiRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntity . + owl:someValuesFrom biolink:SiRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexMolecularMixture ; + rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexMolecularMixture . + owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CommonDataElement ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CommonDataElement . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:IndividualOrganism ; + rdfs:subClassOf biolink:OrganismalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IndividualOrganism . + owl:someValuesFrom biolink:OrganismalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + rdfs:subClassOf biolink:ProteinDomain ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + owl:someValuesFrom biolink:ProteinDomain . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularComplex ; + rdfs:subClassOf biolink:LifeStage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularComplex . + owl:someValuesFrom biolink:LifeStage . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence . + owl:someValuesFrom biolink:SensitivityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:LogOddsAnalysisResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LogOddsAnalysisResult . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Outcome . [] a owl:Restriction ; - rdfs:subClassOf biolink:Disease ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Disease . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugLabel ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugLabel . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicBackgroundExposure ; + rdfs:subClassOf biolink:Zygosity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicBackgroundExposure . + owl:someValuesFrom biolink:Zygosity . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Drug ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Drug . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalCourse ; + rdfs:subClassOf biolink:PosttranslationalModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalCourse . + owl:someValuesFrom biolink:PosttranslationalModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; + rdfs:subClassOf biolink:SequenceVariant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . + owl:someValuesFrom biolink:SequenceVariant . [] a owl:Restriction ; - rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . + owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicExposure ; + rdfs:subClassOf biolink:Cohort ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicExposure . + owl:someValuesFrom biolink:Cohort . [] a owl:Restriction ; - rdfs:subClassOf biolink:ContributorAssociation ; + rdfs:subClassOf biolink:PhenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ContributorAssociation . + owl:someValuesFrom biolink:PhenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; + rdfs:subClassOf biolink:Treatment ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + owl:someValuesFrom biolink:Treatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxon ; + rdfs:subClassOf biolink:ConfidenceLevel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxon . + owl:someValuesFrom biolink:ConfidenceLevel . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; + rdfs:subClassOf biolink:GeneFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . + owl:someValuesFrom biolink:GeneFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalTrial ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalTrial . + owl:someValuesFrom biolink:ChemicalToChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SiRNA ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SiRNA . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + rdfs:subClassOf biolink:MaterialSample ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + owl:someValuesFrom biolink:MaterialSample . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReagentTargetedGene ; + rdfs:subClassOf biolink:CodingSequence ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReagentTargetedGene . + owl:someValuesFrom biolink:CodingSequence . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexChemicalExposure ; + rdfs:subClassOf biolink:ProteinFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexChemicalExposure . + owl:someValuesFrom biolink:ProteinFamily . [] a owl:Restriction ; rdfs:subClassOf biolink:PairwiseMolecularInteraction ; @@ -13325,39 +13155,39 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:PairwiseMolecularInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:PlanetaryEntity ; + rdfs:subClassOf biolink:WebPage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PlanetaryEntity . + owl:someValuesFrom biolink:WebPage . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + rdfs:subClassOf biolink:Publication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . + owl:someValuesFrom biolink:Publication . [] a owl:Restriction ; - rdfs:subClassOf biolink:Behavior ; + rdfs:subClassOf biolink:ContributorAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Behavior . + owl:someValuesFrom biolink:ContributorAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CodingSequence ; + rdfs:subClassOf biolink:PlanetaryEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CodingSequence . + owl:someValuesFrom biolink:PlanetaryEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFeature ; + rdfs:subClassOf biolink:CellularOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFeature . + owl:someValuesFrom biolink:CellularOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismAttribute ; + rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismAttribute . + owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Study ; + rdfs:subClassOf biolink:Gene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Study . + owl:someValuesFrom biolink:Gene . [] a owl:Restriction ; rdfs:subClassOf biolink:Snv ; @@ -13365,400 +13195,538 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Snv . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MicroRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . + owl:someValuesFrom biolink:MicroRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:Fungus ; + rdfs:subClassOf biolink:BiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Fungus . + owl:someValuesFrom biolink:BiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:in_taxon_label ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon . + rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:EvidenceType ; + rdfs:subClassOf biolink:FoodAdditive ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EvidenceType . + owl:someValuesFrom biolink:FoodAdditive . [] a owl:Restriction ; - rdfs:subClassOf biolink:Activity ; + rdfs:subClassOf biolink:NucleosomeModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Activity . + owl:someValuesFrom biolink:NucleosomeModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; + rdfs:subClassOf biolink:Fungus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + owl:someValuesFrom biolink:Fungus . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysicalEntity ; + rdfs:subClassOf biolink:StudyResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysicalEntity . + owl:someValuesFrom biolink:StudyResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceAssociation ; + rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceAssociation . + owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:expression_site ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:expression_site ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:phenotypic_state ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phenotypic_state ] ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin . + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Entity ; + rdfs:subClassOf biolink:ProcessedMaterial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Entity . + owl:someValuesFrom biolink:ProcessedMaterial . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChiSquaredAnalysisResult . + owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularComponent ; + rdfs:subClassOf biolink:StudyVariable ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularComponent . + owl:someValuesFrom biolink:StudyVariable . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genotype ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genotype . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:SmallMolecule ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:SmallMolecule . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalAttribute ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalAttribute . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Vertebrate ; + rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Vertebrate . + owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalEntity ; + rdfs:subClassOf biolink:Bacterium ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalEntity . + owl:someValuesFrom biolink:Bacterium . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalExposure ; + rdfs:subClassOf biolink:ClinicalModifier ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalExposure . + owl:someValuesFrom biolink:ClinicalModifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThing ; + rdfs:subClassOf biolink:PhysicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThing . + owl:someValuesFrom biolink:PhysicalEntity . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SensitivityQuantifier . + owl:someValuesFrom biolink:GeneProductIsoformMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:SmallMolecule ; + rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SmallMolecule . + owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Haplotype ; + rdfs:subClassOf biolink:LogOddsAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Haplotype . + owl:someValuesFrom biolink:LogOddsAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicAttribute ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicAttribute . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:in_taxon_label ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ThingWithTaxon . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SpecificityQuantifier . + rdfs:subClassOf biolink:PhysiologicalProcess ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhysiologicalProcess . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin . + owl:someValuesFrom biolink:OntologyClass . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocation ; + rdfs:subClassOf biolink:Article ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocation . + owl:someValuesFrom biolink:Article . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; + rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . + owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Onset ; + rdfs:subClassOf biolink:ConceptCountAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Onset . + owl:someValuesFrom biolink:ConceptCountAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariant ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariant . + owl:someValuesFrom biolink:SequenceFeatureRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:CommonDataElement ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CommonDataElement . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyVariable ; + rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyVariable . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation . + rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Pathway ; + rdfs:subClassOf biolink:BehavioralExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Pathway . + owl:someValuesFrom biolink:BehavioralExposure . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RegulatoryRegion ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RegulatoryRegion . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BiologicalProcessOrActivity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PreprintPublication ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PreprintPublication . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Activity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Activity . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Dataset ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Dataset . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EpigenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + rdfs:subClassOf biolink:ChemicalMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + owl:someValuesFrom biolink:ChemicalMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + rdfs:subClassOf biolink:Case ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + owl:someValuesFrom biolink:Case . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + rdfs:subClassOf biolink:SequenceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseAssociation . + owl:someValuesFrom biolink:SequenceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; + rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . + owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessedMaterial ; + rdfs:subClassOf biolink:RNAProductIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessedMaterial . + owl:someValuesFrom biolink:RNAProductIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicExposure ; + rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicExposure . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent . + owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicQuality ; + rdfs:subClassOf biolink:ClinicalIntervention ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicQuality . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + owl:someValuesFrom biolink:ClinicalIntervention . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; + rdfs:subClassOf biolink:AccessibleDnaRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptionFactorBindingSite . + owl:someValuesFrom biolink:AccessibleDnaRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLine ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLine . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathognomonicityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneticInheritance ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneticInheritance . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivity ; + rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivity . + owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PosttranslationalModification ; + rdfs:subClassOf biolink:BiologicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PosttranslationalModification . + owl:someValuesFrom biolink:BiologicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidEntity ; + rdfs:subClassOf biolink:ClinicalMeasurement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidEntity . + owl:someValuesFrom biolink:ClinicalMeasurement . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ] ; + owl:onProperty biolink:synonym ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . + owl:someValuesFrom biolink:GeneProductMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:BookChapter ; + rdfs:subClassOf biolink:DrugLabel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BookChapter . + owl:someValuesFrom biolink:DrugLabel . [] a owl:Restriction ; - rdfs:subClassOf biolink:Gene ; + rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Gene . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalTrial ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalTrial . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PopulationToPopulationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PopulationToPopulationAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Case ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -13771,158 +13739,105 @@ biolink:subject a owl:ObjectProperty ; [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:CaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + rdfs:subClassOf biolink:GrossAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + owl:someValuesFrom biolink:GrossAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToParticipantAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GrossAnatomicalStructure ; + rdfs:subClassOf biolink:MacromolecularComplex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GrossAnatomicalStructure . + owl:someValuesFrom biolink:MacromolecularComplex . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConceptCountAnalysisResult ; + rdfs:subClassOf biolink:Drug ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConceptCountAnalysisResult . + owl:someValuesFrom biolink:Drug . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcess ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcess . + owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + rdfs:subClassOf biolink:Behavior ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToCatalystAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . + owl:someValuesFrom biolink:Behavior . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . + rdfs:subClassOf biolink:GeographicExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeographicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; + rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalStructure . + owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalRole ; + rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalRole . + owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + rdfs:subClassOf biolink:TextMiningResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + owl:someValuesFrom biolink:TextMiningResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; + rdfs:subClassOf biolink:Association ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . + owl:someValuesFrom biolink:Association . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPathwayAssociation ; + rdfs:subClassOf biolink:Book ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPathwayAssociation . + owl:someValuesFrom biolink:Book . [] a owl:Restriction ; - rdfs:subClassOf biolink:Treatment ; + rdfs:subClassOf biolink:Disease ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Treatment . + owl:someValuesFrom biolink:Disease . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetVersion ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetVersion . + owl:someValuesFrom biolink:VariantToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Device ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Device . + owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetDistribution ; + rdfs:subClassOf biolink:EnvironmentalFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetDistribution . + owl:someValuesFrom biolink:EnvironmentalFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; + rdfs:subClassOf biolink:GenomicBackgroundExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . + owl:someValuesFrom biolink:GenomicBackgroundExposure . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation . [] a owl:Restriction ; rdfs:subClassOf biolink:BehavioralFeature ; @@ -13930,628 +13845,724 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:BehavioralFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExonToTranscriptRelationship ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExonToTranscriptRelationship . + owl:someValuesFrom biolink:NoncodingRNAProduct . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom biolink:CellLine ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; + rdfs:subClassOf biolink:EnvironmentalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . + owl:someValuesFrom biolink:EnvironmentalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntity ; + rdfs:subClassOf biolink:GeneToGoTermAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntity . + owl:someValuesFrom biolink:GeneToGoTermAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularEntity ; + rdfs:subClassOf biolink:MolecularActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularEntity . + owl:someValuesFrom biolink:MolecularActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProductIsoform ; + rdfs:subClassOf biolink:SeverityValue ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProductIsoform . + owl:someValuesFrom biolink:SeverityValue . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicSequenceLocalization ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicSequenceLocalization . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyPopulation ; + rdfs:subClassOf biolink:ClinicalAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyPopulation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . + owl:someValuesFrom biolink:ClinicalAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:TextMiningResult ; + rdfs:subClassOf biolink:RetrievalSource ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TextMiningResult . + owl:someValuesFrom biolink:RetrievalSource . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamily ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamily . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + rdfs:subClassOf biolink:AnatomicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToDiseaseAssociation . + owl:someValuesFrom biolink:AnatomicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyResult ; + rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyResult . + owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalEntity ; + rdfs:subClassOf biolink:EntityToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalEntity . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin . + owl:someValuesFrom biolink:EntityToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinFamily ; + rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinFamily . + owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Mammal ; + rdfs:subClassOf biolink:Virus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Mammal . + owl:someValuesFrom biolink:Virus . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MaterialSample ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior . + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; + rdfs:subClassOf biolink:ClinicalFinding ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . + owl:someValuesFrom biolink:ClinicalFinding . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypicSex ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypicSex . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:JournalArticle ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:JournalArticle . [] a owl:Restriction ; - rdfs:subClassOf biolink:Event ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Event . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Article ; + rdfs:subClassOf biolink:Entity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Article . + owl:someValuesFrom biolink:Entity . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Outcome ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicQuality ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicQuality . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Phenomenon ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Phenomenon . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypeToGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypeToGeneAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypeToVariantAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypeToVariantAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeographicLocationAtTime ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeographicLocationAtTime . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:WebPage ; + rdfs:subClassOf biolink:Attribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:WebPage . + owl:someValuesFrom biolink:Attribute . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin . + rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:AdministrativeEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:AdministrativeEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PreprintPublication ; + rdfs:subClassOf biolink:Hospitalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PreprintPublication . + owl:someValuesFrom biolink:Hospitalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . + owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Virus ; + rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Virus . + owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:MolecularEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + owl:someValuesFrom biolink:MolecularEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToPathwayAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToPathwayAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneticInheritance ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneticInheritance . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin . + owl:someValuesFrom biolink:FrequencyQualifierMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProduct ; + rdfs:subClassOf biolink:ChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProduct . + owl:someValuesFrom biolink:ChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Protein ; + rdfs:subClassOf biolink:InformationContentEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Protein . + owl:someValuesFrom biolink:InformationContentEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Book ; + rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Book . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity . + owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent . + rdfs:subClassOf biolink:DrugExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DrugExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Transcript ; + rdfs:subClassOf biolink:BiologicalSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Transcript . + owl:someValuesFrom biolink:BiologicalSex . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . + owl:someValuesFrom biolink:ActivityAndBehavior . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductMixin . + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:VariantToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Cell ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Cell . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:RelationshipQuantifier . + owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysiologicalProcess ; + rdfs:subClassOf biolink:ExonToTranscriptRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysiologicalProcess . + owl:someValuesFrom biolink:ExonToTranscriptRelationship . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismToOrganismAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcess ; + rdfs:subClassOf biolink:EvidenceType ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcess . + owl:someValuesFrom biolink:EvidenceType . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; + rdfs:subClassOf biolink:Genome ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . + owl:someValuesFrom biolink:Genome . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationToPopulationAssociation ; + rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationToPopulationAssociation . + owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:FunctionalAssociation ; + rdfs:subClassOf biolink:Polypeptide ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FunctionalAssociation . + owl:someValuesFrom biolink:Polypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:FoodAdditive ; + rdfs:subClassOf biolink:Exon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FoodAdditive . + owl:someValuesFrom biolink:Exon . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConfidenceLevel ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConfidenceLevel . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:JournalArticle ; + rdfs:subClassOf biolink:Study ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:JournalArticle . + owl:someValuesFrom biolink:Study . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalSex ; + rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalSex . + owl:someValuesFrom biolink:TranscriptionFactorBindingSite . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntity ; + rdfs:subClassOf biolink:PathologicalProcessExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntity . + owl:someValuesFrom biolink:PathologicalProcessExposure . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct . + rdfs:subClassOf biolink:ProteinIsoform ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ProteinIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:Patent ; + rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Patent . + owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Pathway ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Pathway . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + rdfs:subClassOf biolink:GenomicSequenceLocalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivity . + owl:someValuesFrom biolink:GenomicSequenceLocalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:TaxonToTaxonAssociation ; + rdfs:subClassOf biolink:Agent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TaxonToTaxonAssociation . + owl:someValuesFrom biolink:Agent . [] a owl:Restriction ; - rdfs:subClassOf biolink:RegulatoryRegion ; + rdfs:subClassOf biolink:Invertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RegulatoryRegion . + owl:someValuesFrom biolink:Invertebrate . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:frequency_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:frequency_qualifier ] ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_percentage ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . + owl:someValuesFrom biolink:FrequencyQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularMixture ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularMixture . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:RelationshipQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinDomain ; + rdfs:subClassOf biolink:GenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinDomain . + owl:someValuesFrom biolink:GenotypicSex . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:DrugToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:DrugToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; + rdfs:subClassOf biolink:Device ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToDiseaseAssociation . + owl:someValuesFrom biolink:Device . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cell ; + rdfs:subClassOf biolink:Mammal ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cell . + owl:someValuesFrom biolink:Mammal . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiagnosticAid ; + rdfs:subClassOf biolink:OrganismAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiagnosticAid . + owl:someValuesFrom biolink:OrganismAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + rdfs:subClassOf biolink:FunctionalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + owl:someValuesFrom biolink:FunctionalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . + owl:someValuesFrom biolink:ReactionToParticipantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + owl:someValuesFrom biolink:DrugToGeneInteractionExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; + rdfs:subClassOf biolink:TranscriptToGeneRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NoncodingRNAProduct . + owl:someValuesFrom biolink:TranscriptToGeneRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinIsoform ; + rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinIsoform . + owl:someValuesFrom biolink:ChiSquaredAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:Association ; + rdfs:subClassOf biolink:PathologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Association . + owl:someValuesFrom biolink:PathologicalProcess . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ComplexChemicalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ComplexChemicalExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Patent ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Patent . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Event ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Event . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . diff --git a/project/shacl/biolink_model.shacl.ttl b/project/shacl/biolink_model.shacl.ttl index f92a85b41..459173163 100644 --- a/project/shacl/biolink_model.shacl.ttl +++ b/project/shacl/biolink_model.shacl.ttl @@ -10,34 +10,45 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -45,55 +56,44 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:order 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:AccessibleDnaRegion . biolink:Activity a sh:NodeShape ; @@ -101,12 +101,15 @@ biolink:Activity a sh:NodeShape ; sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -114,59 +117,56 @@ biolink:Activity a sh:NodeShape ; sh:order 2 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ] ; sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; @@ -177,89 +177,91 @@ biolink:ActivityAndBehavior a sh:NodeShape ; biolink:AdministrativeEntity a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( rdf:type biolink:address biolink:affiliation ) ; + sh:ignoredProperties ( biolink:affiliation rdf:type biolink:address ) ; sh:property [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ] ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -267,72 +269,38 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -340,109 +308,127 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -450,119 +436,60 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ] ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -575,45 +502,38 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -623,57 +543,69 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; @@ -685,258 +617,326 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:original_object ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the part" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the whole" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the part" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . - + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the whole" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + biolink:Annotation a sh:NodeShape ; sh:closed false ; sh:description "Biolink Model root class for entity annotations." ; - sh:ignoredProperties ( rdf:type biolink:has_unit biolink:has_numeric_value ) ; + sh:ignoredProperties ( biolink:has_numeric_value biolink:has_unit rdf:type ) ; sh:targetClass biolink:Annotation . biolink:Article a sh:NodeShape ; @@ -944,64 +944,113 @@ biolink:Article a sh:NodeShape ; sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], + sh:order 3 ; + sh:path biolink:issue ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:volume ], + sh:order 19 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:format ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path rdfs:label ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:summary ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:issue ], + sh:order 12 ; + sh:path biolink:rights ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:iri ], + sh:order 23 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; @@ -1009,126 +1058,54 @@ biolink:Article a sh:NodeShape ; sh:order 10 ; sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:rights ], + sh:order 21 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:id ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ] ; + sh:order 2 ; + sh:path biolink:volume ] ; sh:targetClass biolink:Article . biolink:Association a sh:NodeShape ; sh:closed true ; sh:description "A typed association between two entities, supported by evidence" ; - sh:ignoredProperties ( biolink:subject_form_or_variant_qualifier biolink:max_research_phase biolink:object_part_qualifier biolink:object_form_or_variant_qualifier biolink:population_context_qualifier biolink:temporal_context_qualifier biolink:phase biolink:anatomical_context_qualifier biolink:object_derivative_qualifier biolink:clinical_approval_status biolink:stoichiometry biolink:object_direction_qualifier biolink:reaction_side biolink:stage_qualifier biolink:disease_context_qualifier biolink:reaction_direction biolink:start_interbase_coordinate biolink:genome_build biolink:object_aspect_qualifier biolink:subject_derivative_qualifier biolink:catalyst_qualifier biolink:has_percentage biolink:quantifier_qualifier biolink:onset_qualifier biolink:strand biolink:associated_environmental_context biolink:has_total biolink:subject_direction_qualifier biolink:end_interbase_coordinate biolink:has_quotient rdf:type biolink:subject_context_qualifier biolink:subject_part_qualifier biolink:causal_mechanism_qualifier biolink:phenotypic_state biolink:subject_aspect_qualifier biolink:object_context_qualifier biolink:sex_qualifier biolink:has_count biolink:species_context_qualifier biolink:frequency_qualifier biolink:qualified_predicate biolink:expression_site biolink:interacting_molecules_category biolink:FDA_adverse_event_level ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:ignoredProperties ( biolink:subject_direction_qualifier biolink:reaction_side biolink:temporal_context_qualifier biolink:sex_qualifier biolink:species_context_qualifier biolink:anatomical_context_qualifier biolink:subject_aspect_qualifier biolink:reaction_direction biolink:object_form_or_variant_qualifier biolink:strand biolink:onset_qualifier biolink:disease_context_qualifier biolink:has_total biolink:subject_derivative_qualifier biolink:object_direction_qualifier biolink:subject_form_or_variant_qualifier biolink:clinical_approval_status biolink:object_derivative_qualifier biolink:subject_context_qualifier biolink:has_count biolink:catalyst_qualifier biolink:start_interbase_coordinate biolink:stage_qualifier biolink:phenotypic_state biolink:quantifier_qualifier biolink:stoichiometry biolink:subject_part_qualifier biolink:qualified_predicate biolink:has_percentage biolink:max_research_phase biolink:object_aspect_qualifier biolink:associated_environmental_context biolink:phase biolink:FDA_adverse_event_level biolink:interacting_molecules_category biolink:frequency_qualifier biolink:population_context_qualifier biolink:object_part_qualifier biolink:expression_site biolink:end_interbase_coordinate biolink:has_quotient biolink:object_context_qualifier biolink:genome_build biolink:causal_mechanism_qualifier rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -1136,60 +1113,40 @@ biolink:Association a sh:NodeShape ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -1203,164 +1160,210 @@ biolink:Association a sh:NodeShape ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; - sh:path biolink:subject_label_closure ] ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:Association . biolink:Bacterium a sh:NodeShape ; sh:closed true ; sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -1373,108 +1376,109 @@ biolink:Bacterium a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Bacterium . biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], + sh:property [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], [ sh:class biolink:BehavioralFeature ; sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; @@ -1482,45 +1486,57 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -1528,18 +1544,34 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; @@ -1553,48 +1585,17 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:order 44 ; sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 45 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; @@ -1602,132 +1603,146 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:order 4 ; sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], + sh:order 43 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_total ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ] ; + sh:order 38 ; + sh:path dct:description ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ] ; sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . biolink:BehavioralExposure a sh:NodeShape ; sh:closed true ; sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -1735,67 +1750,52 @@ biolink:BehavioralExposure a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ] ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:BehavioralExposure . biolink:BehavioralOutcome a sh:NodeShape ; @@ -1806,27 +1806,50 @@ biolink:BehavioralOutcome a sh:NodeShape ; biolink:BiologicalEntity a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( biolink:has_input rdf:type biolink:symbol biolink:has_gene biolink:has_zygosity biolink:has_biological_sequence biolink:has_output biolink:has_gene_or_gene_product biolink:enabled_by ) ; - sh:property [ sh:datatype xsd:string ; + sh:ignoredProperties ( biolink:has_input biolink:enabled_by biolink:has_gene biolink:has_biological_sequence biolink:symbol biolink:has_gene_or_gene_product biolink:has_zygosity biolink:has_output rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -1839,106 +1862,93 @@ biolink:BiologicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:BiologicalEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:closed true ; sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:enabled_by ], + sh:order 1 ; + sh:path biolink:has_output ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_input ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_input ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -1947,43 +1957,33 @@ biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:order 3 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_output ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ] ; + sh:order 16 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:BiologicalProcessOrActivity . biolink:BioticExposure a sh:NodeShape ; @@ -1995,53 +1995,47 @@ biolink:BioticExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -2049,11 +2043,10 @@ biolink:BioticExposure a sh:NodeShape ; sh:order 5 ; sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; @@ -2065,29 +2058,65 @@ biolink:BioticExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ] ; + sh:order 0 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:BioticExposure . biolink:Book a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Agent ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; @@ -2098,55 +2127,51 @@ biolink:Book a sh:NodeShape ; sh:order 7 ; sh:path biolink:license ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Books should have industry-standard identifier such as from ISBN." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Should generally be set to an ontology class defined term for 'book'." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -2154,22 +2179,18 @@ biolink:Book a sh:NodeShape ; sh:order 21 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; @@ -2177,58 +2198,47 @@ biolink:Book a sh:NodeShape ; sh:order 2 ; sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ] ; + sh:order 12 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Book . biolink:BookChapter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:keywords ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:creation_date ], + sh:order 21 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:rights ], + sh:order 4 ; + sh:path biolink:pages ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; @@ -2236,105 +2246,78 @@ biolink:BookChapter a sh:NodeShape ; sh:order 5 ; sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:description "chapter of a book" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:chapter ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 14 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:volume ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "chapter of a book" ; - sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:chapter ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:provided_by ], + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:license ], + sh:order 18 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; @@ -2342,30 +2325,40 @@ biolink:BookChapter a sh:NodeShape ; sh:order 9 ; sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:pages ], + sh:order 17 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:full_name ] ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:mesh_terms ] ; sh:targetClass biolink:BookChapter . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An abstract association for use where the case is the subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -2378,28 +2371,104 @@ biolink:CaseToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:CaseToEntityAssociationMixin . biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -2407,40 +2476,112 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -2448,17 +2589,17 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -2466,10 +2607,22 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 5 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_total ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -2477,12 +2630,34 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:order 43 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -2496,323 +2671,221 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . + +biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; + sh:order 46 ; sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; + sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; + sh:order 48 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:path biolink:timepoint ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ] ; - sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . - -biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -2820,85 +2893,62 @@ biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:order 40 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 43 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 45 ; + sh:path biolink:has_quotient ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 44 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -2906,121 +2956,82 @@ biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:order 20 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ] ; + sh:path biolink:qualifier ] ; sh:targetClass biolink:CausalGeneToDiseaseAssociation . biolink:Cell a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -3028,197 +3039,137 @@ biolink:Cell a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:Cell . biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -3226,247 +3177,213 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 44 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; - sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . - -biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; - sh:ignoredProperties ( biolink:subject_direction_qualifier biolink:object_direction_qualifier biolink:frequency_qualifier rdf:type biolink:qualified_predicate biolink:object_aspect_qualifier biolink:subject_aspect_qualifier ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; + sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + +biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + sh:ignoredProperties ( biolink:object_aspect_qualifier biolink:subject_direction_qualifier biolink:object_direction_qualifier biolink:subject_aspect_qualifier biolink:frequency_qualifier biolink:qualified_predicate rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -3474,35 +3391,99 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; @@ -3514,53 +3495,65 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ] ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An relationship between a cell line and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -3573,40 +3566,37 @@ biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:CellLineToEntityAssociationMixin . biolink:CellularOrganism a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -3614,201 +3604,222 @@ biolink:CellularOrganism a sh:NodeShape ; sh:order 4 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:CellularOrganism . biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:object_namespace ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 26 ; sh:path biolink:knowledge_level ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 17 ; + sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 45 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 53 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:object_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:adjusted_p_value ], + sh:order 35 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:retrieval_source_ids ], + sh:order 13 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path rdfs:label ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:primary_knowledge_source ], + sh:order 51 ; + sh:path dct:description ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:qualifier ], + sh:order 29 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path dct:description ], + sh:order 23 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:iri ], + sh:order 40 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OrganismTaxon ; sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; @@ -3816,225 +3827,150 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], + sh:order 25 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 17 ; - sh:path rdf:object ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:order 47 ; + sh:path biolink:iri ], [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:in ( "metabolite" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:original_subject ], + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 24 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:p_value ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 16 ; + sh:path rdf:predicate ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path rdf:subject ], + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:qualified_predicate ], + sh:order 31 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 52 ; sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 46 ; + sh:path biolink:id ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 48 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 30 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 37 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; + sh:order 15 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . + +biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -4047,45 +3983,32 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -4097,17 +4020,28 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -4115,56 +4049,119 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -4173,70 +4170,101 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; + sh:order 4 ; + sh:path biolink:qualifier ] ; sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "A regulatory relationship between two genes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -4249,53 +4277,88 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 34 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:subject_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "the direction is always from regulator to regulated" ; sh:maxCount 1 ; @@ -4303,130 +4366,67 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; @@ -4439,7 +4439,14 @@ biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An interaction between a chemical entity and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -4452,461 +4459,459 @@ biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:predicate ] ; sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . biolink:ChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A chemical exposure is an intake of a particular chemical entity." ; - sh:ignoredProperties ( rdf:type biolink:has_gene_or_gene_product ) ; + sh:ignoredProperties ( biolink:has_gene_or_gene_product rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ] ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ChemicalExposure . biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:closed true ; sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_object ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:subject_context_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path dct:description ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], + sh:order 22 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:category ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:subject ], + sh:order 45 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:id ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], + sh:order 28 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path rdf:type ], + sh:order 16 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 10 ; + sh:path rdf:object ], [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:in ( "metabolite" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_derivative_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:primary_knowledge_source ], + sh:order 21 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:agent_type ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], + sh:order 24 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 17 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 38 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:publications ], + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], + sh:order 31 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_subject ], + sh:order 12 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:negated ], + sh:order 44 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:AnatomicalEntity ; sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:knowledge_source ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:object_part_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:agent_type ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 10 ; - sh:path rdf:object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path rdf:predicate ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:AnatomicalEntity ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], + sh:order 33 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path biolink:deprecated ] ; + sh:targetClass biolink:ChemicalGeneInteractionAssociation . + +biolink:ChemicalMixture a sh:NodeShape ; + sh:closed true ; + sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:predicate ], + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:ChemicalGeneInteractionAssociation . - -biolink:ChemicalMixture a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:synonym ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:boolean ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:deprecated ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], + sh:order 15 ; + sh:path biolink:category ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; @@ -4914,39 +4919,34 @@ biolink:ChemicalMixture a sh:NodeShape ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path dct:description ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:ChemicalMixture . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; @@ -4958,51 +4958,96 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:closed true ; sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "" ; sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:FDA_adverse_event_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path dct:description ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -5011,45 +5056,44 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:order 32 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -5062,130 +5106,86 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ] ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; @@ -5193,38 +5193,27 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -5232,227 +5221,229 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 35 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ] ; + sh:order 39 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; - sh:ignoredProperties ( biolink:stoichiometry rdf:type biolink:reaction_side biolink:reaction_direction biolink:catalyst_qualifier ) ; + sh:ignoredProperties ( biolink:reaction_side biolink:catalyst_qualifier biolink:reaction_direction biolink:stoichiometry rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -5460,44 +5451,91 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:order 36 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; @@ -5509,35 +5547,52 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -5545,462 +5600,300 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:order 19 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:ChemicalToChemicalAssociation . biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:closed true ; sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 35 ; + sh:path rdf:type ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; + sh:description "the downstream chemical entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 36 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:catalyst_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the upstream chemical entity" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . - -biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 5 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 21 ; sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 39 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; + sh:order 25 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ] ; + sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . + +biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -6008,81 +5901,64 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; @@ -6090,176 +5966,252 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An interaction between a chemical entity and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:ChemicalToEntityAssociationMixin . - -biolink:ChemicalToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a chemical entity and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + +biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An interaction between a chemical entity and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:ChemicalToEntityAssociationMixin . + +biolink:ChemicalToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a chemical entity and a biological process or pathway." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6267,16 +6219,30 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -6289,113 +6255,151 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that is affected by the chemical" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ] ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:ChemicalToPathwayAssociation . biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6403,65 +6407,61 @@ biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:ChiSquaredAnalysisResult . biolink:ClinicalCourse a sh:NodeShape ; @@ -6469,125 +6469,120 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:ClinicalCourse . biolink:ClinicalEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6595,37 +6590,42 @@ biolink:ClinicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ] ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ClinicalEntity . biolink:ClinicalFinding a sh:NodeShape ; @@ -6633,66 +6633,66 @@ biolink:ClinicalFinding a sh:NodeShape ; sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -6715,11 +6715,12 @@ biolink:ClinicalFinding a sh:NodeShape ; biolink:ClinicalIntervention a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6727,61 +6728,60 @@ biolink:ClinicalIntervention a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:ClinicalIntervention . biolink:ClinicalMeasurement a sh:NodeShape ; @@ -6789,28 +6789,34 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -6828,130 +6834,85 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:ClinicalMeasurement . - -biolink:ClinicalModifier a sh:NodeShape ; - sh:closed true ; - sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path dct:description ] ; + sh:targetClass biolink:ClinicalMeasurement . + +biolink:ClinicalModifier a sh:NodeShape ; + sh:closed true ; + sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -6963,58 +6924,94 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:ClinicalModifier . - -biolink:ClinicalTrial a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; + sh:path biolink:id ] ; + sh:targetClass biolink:ClinicalModifier . + +biolink:ClinicalTrial a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -7022,20 +7019,23 @@ biolink:ClinicalTrial a sh:NodeShape ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ClinicalTrial . biolink:CodingSequence a sh:NodeShape ; @@ -7047,11 +7047,17 @@ biolink:CodingSequence a sh:NodeShape ; sh:order 3 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -7059,156 +7065,150 @@ biolink:CodingSequence a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; - sh:targetClass biolink:CodingSequence . - -biolink:Cohort a sh:NodeShape ; - sh:closed true ; - sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 14 ; sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ] ; + sh:targetClass biolink:CodingSequence . + +biolink:Cohort a sh:NodeShape ; + sh:closed true ; + sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Cohort . biolink:CommonDataElement a sh:NodeShape ; @@ -7216,20 +7216,19 @@ biolink:CommonDataElement a sh:NodeShape ; sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -7237,33 +7236,50 @@ biolink:CommonDataElement a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -7286,23 +7302,7 @@ biolink:CommonDataElement a sh:NodeShape ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:CommonDataElement . biolink:ComplexChemicalExposure a sh:NodeShape ; @@ -7314,15 +7314,13 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -7330,27 +7328,21 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:order 4 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -7358,42 +7350,50 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:ComplexChemicalExposure . biolink:ComplexMolecularMixture a sh:NodeShape ; @@ -7401,15 +7401,53 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:iri ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; @@ -7421,75 +7459,44 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:order 8 ; sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:order 18 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 12 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -7497,58 +7504,74 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:ComplexMolecularMixture . biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -7559,66 +7582,54 @@ biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ] ; + sh:order 9 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ConceptCountAnalysisResult . biolink:ConfidenceLevel a sh:NodeShape ; sh:closed true ; sh:description "Level of confidence in a statement" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -7626,21 +7637,33 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 9 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -7654,260 +7677,232 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 12 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:ConfidenceLevel . biolink:ContributorAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:InformationContentEntity ; + sh:description "information content entity which an agent has helped realise" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Agent ; + sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:InformationContentEntity ; - sh:description "information content entity which an agent has helped realise" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -7915,11 +7910,16 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -7936,16 +7936,29 @@ biolink:ContributorAssociation a sh:NodeShape ; biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -7953,203 +7966,130 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], + sh:order 40 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to correlate with the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:double ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to correlate with the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 44 ; + sh:path biolink:has_total ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -8157,180 +8097,240 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 46 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], + sh:order 36 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ] ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . biolink:DatasetSummary a sh:NodeShape ; sh:closed true ; sh:description "an item that holds summary level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:creation_date ], + sh:order 4 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:source_web_page ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path schema1:logo ], + sh:order 2 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:source_web_page ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path schema1:logo ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:format ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:license ], + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:creation_date ] ; sh:targetClass biolink:DatasetSummary . biolink:DatasetVersion a sh:NodeShape ; @@ -8338,97 +8338,86 @@ biolink:DatasetVersion a sh:NodeShape ; sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:ingest_date ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:ingest_date ], + sh:order 14 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:creation_date ], + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:class biolink:DatasetDistribution ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], + sh:order 18 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:license ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:creation_date ], + [ sh:class biolink:DatasetDistribution ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path dct:distribution ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], [ sh:class biolink:Dataset ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; @@ -8439,7 +8428,18 @@ biolink:DatasetVersion a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path dct:description ] ; sh:targetClass biolink:DatasetVersion . biolink:DiagnosticAid a sh:NodeShape ; @@ -8447,19 +8447,22 @@ biolink:DiagnosticAid a sh:NodeShape ; sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -8467,34 +8470,32 @@ biolink:DiagnosticAid a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -8502,114 +8503,113 @@ biolink:DiagnosticAid a sh:NodeShape ; sh:order 9 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ] ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:DiagnosticAid . biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:closed true ; sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ] ; + sh:order 1 ; + sh:path rdfs:label ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; @@ -8621,7 +8621,14 @@ biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -8634,14 +8641,7 @@ biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape ; @@ -8653,28 +8653,18 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -8687,45 +8677,57 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -8738,17 +8740,6 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -8756,278 +8747,307 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:GeneticInheritance ; + sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path biolink:adjusted_p_value ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + +biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:GeneticInheritance ; - sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . - -biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -9039,67 +9059,47 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; + sh:order 7 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; @@ -9133,154 +9133,103 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:description "An association between an exposure event and a disease." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -9288,18 +9237,17 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -9307,207 +9255,134 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:DiseaseToExposureEventAssociation . - -biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 24 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:agent_type ], + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; - sh:path biolink:subject_closure ], + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; + sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 44 ; + sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Disease ; sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path rdf:type ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:qualified_predicate ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:DiseaseToExposureEventAssociation . + +biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:negated ], + sh:order 41 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:id ], + sh:order 35 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:object_category_closure ], + sh:order 11 ; + sh:path biolink:qualifier ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9515,224 +9390,326 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path rdf:object ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 32 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 49 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:publications ], + sh:order 20 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 1 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 31 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 21 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 50 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; + sh:order 14 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:onset_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence ], + sh:order 29 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:p_value ], + sh:order 40 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:adjusted_p_value ], + sh:order 39 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_count ], + sh:order 2 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path rdfs:label ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:order 46 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:object_direction_qualifier ], + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . - -biolink:DrugExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A drug exposure is an intake of a particular drug." ; - sh:ignoredProperties ( rdf:type biolink:has_gene_or_gene_product ) ; - sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 38 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 42 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:timepoint ], + sh:path biolink:onset_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:negated ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:disease_context_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 44 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; + sh:order 30 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:publications ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path biolink:frequency_qualifier ] ; + sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . + +biolink:DrugExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A drug exposure is an intake of a particular drug." ; + sh:ignoredProperties ( biolink:has_gene_or_gene_product rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path biolink:has_quantitative_value ], + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -9740,22 +9717,45 @@ biolink:DrugExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 9 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:DrugExposure . biolink:DrugLabel a sh:NodeShape ; @@ -9763,54 +9763,64 @@ biolink:DrugLabel a sh:NodeShape ; sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 18 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -9818,77 +9828,74 @@ biolink:DrugLabel a sh:NodeShape ; sh:order 10 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:format ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ] ; + sh:order 8 ; + sh:path biolink:rights ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An interaction between a drug and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -9901,187 +9908,148 @@ biolink:DrugToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:DrugToEntityAssociationMixin . biolink:DrugToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product that is affected by the drug" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product that is affected by the drug" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -10089,98 +10057,123 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ] ; + sh:order 14 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:DrugToGeneAssociation . biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:closed true ; sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path biolink:full_name ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -10188,295 +10181,300 @@ biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:category ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:timepoint ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:iri ] ; sh:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ], + sh:order 41 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "connects an association to an instance of supporting evidence" ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 38 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 6 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 39 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 36 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_count ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 46 ; + sh:path biolink:has_percentage ], + [ sh:description "connects an association to an instance of supporting evidence" ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 44 ; + sh:path biolink:has_total ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; sh:maxCount 1 ; @@ -10484,37 +10482,28 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -10522,6 +10511,11 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -10530,28 +10524,45 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ] ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:DruggableGeneToDiseaseAssociation . biolink:Entity a sh:NodeShape ; sh:closed false ; sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; - sh:ignoredProperties ( biolink:max_research_phase biolink:has_quantitative_value biolink:trade_name biolink:object_part_qualifier biolink:iso_abbreviation biolink:has_zygosity biolink:has_device biolink:anatomical_context_qualifier biolink:object_derivative_qualifier biolink:has_input biolink:stoichiometry biolink:upstream_resource_ids biolink:primary_knowledge_source biolink:reaction_side biolink:is_supplement biolink:has_supporting_studies biolink:reaction_direction biolink:start_interbase_coordinate biolink:available_from biolink:has_procedure rdf:predicate biolink:has_percentage biolink:associated_environmental_context biolink:has_total biolink:summary biolink:subject_part_qualifier biolink:has_biological_sequence biolink:resource_id biolink:timepoint biolink:published_in biolink:rights biolink:frequency_qualifier biolink:qualified_predicate biolink:xref biolink:is_metabolite biolink:object_namespace biolink:FDA_adverse_event_level biolink:object_category_closure biolink:knowledge_source biolink:temporal_context_qualifier biolink:has_dataset biolink:full_name biolink:latitude biolink:object_direction_qualifier biolink:format biolink:longitude biolink:keywords biolink:source_web_page biolink:onset_qualifier biolink:subject_direction_qualifier biolink:chapter biolink:subject_context_qualifier biolink:knowledge_level biolink:subject_label_closure biolink:has_evidence biolink:has_drug biolink:qualifier biolink:publications biolink:object_context_qualifier biolink:aggregator_knowledge_source biolink:subject_namespace biolink:resource_role biolink:qualifiers biolink:license biolink:in_taxon biolink:pages biolink:original_subject biolink:ingest_date biolink:has_chemical_role biolink:object_category biolink:drug_regulatory_status_world_wide biolink:address biolink:authors biolink:population_context_qualifier biolink:enabled_by biolink:phase biolink:agent_type biolink:has_qualitative_value biolink:is_toxic biolink:has_gene biolink:genome_build biolink:subject_derivative_qualifier biolink:adjusted_p_value biolink:distribution_download_url biolink:affiliation biolink:quantifier_qualifier biolink:has_gene_or_gene_product biolink:has_taxonomic_rank biolink:causal_mechanism_qualifier biolink:in_taxon_label biolink:phenotypic_state biolink:subject_aspect_qualifier biolink:subject_category biolink:issue biolink:sex_qualifier biolink:has_count biolink:interacting_molecules_category biolink:mesh_terms biolink:subject_form_or_variant_qualifier biolink:retrieval_source_ids biolink:synonym dct:distribution biolink:symbol biolink:object_form_or_variant_qualifier biolink:has_attribute_type biolink:has_output biolink:clinical_approval_status biolink:original_object biolink:volume schema1:logo biolink:max_tolerated_dose rdf:subject biolink:creation_date biolink:stage_qualifier biolink:disease_context_qualifier biolink:p_value biolink:object_closure biolink:highest_FDA_approval_status rdf:object biolink:object_aspect_qualifier biolink:subject_closure biolink:catalyst_qualifier biolink:strand dct:type biolink:end_interbase_coordinate biolink:has_quotient rdf:type biolink:object_label_closure biolink:negated biolink:original_predicate biolink:subject_category_closure biolink:species_context_qualifier biolink:routes_of_delivery biolink:expression_site biolink:provided_by ) ; - sh:property [ sh:class biolink:Attribute ; + sh:ignoredProperties ( biolink:upstream_resource_ids biolink:authors biolink:temporal_context_qualifier biolink:species_context_qualifier biolink:trade_name biolink:object_form_or_variant_qualifier biolink:routes_of_delivery biolink:onset_qualifier biolink:has_supporting_studies biolink:strand biolink:original_predicate biolink:provided_by biolink:subject_form_or_variant_qualifier biolink:clinical_approval_status biolink:has_evidence biolink:phenotypic_state biolink:max_research_phase biolink:has_biological_sequence biolink:license biolink:FDA_adverse_event_level biolink:available_from biolink:summary biolink:ingest_date biolink:subject_category_closure biolink:has_gene biolink:has_procedure biolink:iso_abbreviation biolink:object_closure rdf:type biolink:subject_closure biolink:highest_FDA_approval_status biolink:subject_category biolink:has_attribute_type biolink:has_total biolink:in_taxon biolink:object_namespace biolink:max_tolerated_dose biolink:has_count biolink:knowledge_source biolink:affiliation biolink:qualifiers biolink:enabled_by biolink:chapter biolink:p_value biolink:has_gene_or_gene_product biolink:primary_knowledge_source biolink:resource_role biolink:volume biolink:has_input rdf:predicate biolink:object_category_closure biolink:population_context_qualifier biolink:object_part_qualifier biolink:is_toxic biolink:original_subject rdf:subject biolink:retrieval_source_ids biolink:subject_namespace biolink:creation_date biolink:reaction_side biolink:sex_qualifier biolink:anatomical_context_qualifier biolink:format biolink:has_output biolink:mesh_terms schema1:logo biolink:has_quantitative_value biolink:issue biolink:object_direction_qualifier dct:distribution biolink:subject_context_qualifier biolink:catalyst_qualifier biolink:stage_qualifier biolink:quantifier_qualifier biolink:stoichiometry biolink:subject_part_qualifier biolink:agent_type biolink:has_percentage biolink:in_taxon_label biolink:synonym biolink:publications biolink:phase biolink:timepoint biolink:pages biolink:is_metabolite biolink:has_drug biolink:symbol biolink:longitude biolink:causal_mechanism_qualifier dct:type biolink:object_label_closure biolink:published_in biolink:has_chemical_role biolink:subject_direction_qualifier biolink:knowledge_level biolink:rights biolink:object_category biolink:subject_aspect_qualifier biolink:adjusted_p_value biolink:reaction_direction biolink:disease_context_qualifier biolink:latitude biolink:subject_label_closure biolink:aggregator_knowledge_source biolink:original_object biolink:subject_derivative_qualifier biolink:qualifier biolink:object_derivative_qualifier biolink:start_interbase_coordinate biolink:qualified_predicate rdf:object biolink:has_qualitative_value biolink:is_supplement biolink:object_aspect_qualifier biolink:resource_id biolink:source_web_page biolink:associated_environmental_context biolink:has_dataset biolink:address biolink:interacting_molecules_category biolink:frequency_qualifier biolink:drug_regulatory_status_world_wide biolink:keywords biolink:has_taxonomic_rank biolink:expression_site biolink:xref biolink:end_interbase_coordinate biolink:has_quotient biolink:full_name biolink:has_device biolink:negated biolink:has_zygosity biolink:object_context_qualifier biolink:distribution_download_url biolink:genome_build ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -10560,11 +10571,11 @@ biolink:Entity a sh:NodeShape ; sh:order 0 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -10574,84 +10585,41 @@ biolink:Entity a sh:NodeShape ; [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:category ] ; + sh:path rdf:type ] ; sh:targetClass biolink:Entity . biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -10659,170 +10627,202 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], + sh:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:object_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 8 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ] ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:max_research_phase ] ; sh:targetClass biolink:EntityToDiseaseAssociation . biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; @@ -10830,18 +10830,16 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:description "mixin class for any association whose object (target node) is a disease" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10849,60 +10847,62 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ] ; + sh:order 7 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10942,24 +10942,14 @@ biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for entity to disease or phenotype associations." ; - sh:ignoredProperties ( biolink:sex_qualifier biolink:has_count biolink:has_total biolink:has_quotient rdf:type biolink:disease_context_qualifier biolink:has_percentage ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:ignoredProperties ( biolink:has_percentage biolink:has_quotient biolink:sex_qualifier biolink:has_count biolink:disease_context_qualifier rdf:type biolink:has_total ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10967,44 +10957,61 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:predicate ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ] ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ] ; sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between some entity and an outcome" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -11017,128 +11024,64 @@ biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:EntityToOutcomeAssociationMixin . biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], + sh:order 8 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -11146,300 +11089,325 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], [ sh:description "" ; sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:clinical_approval_status ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:order 6 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:order 1 ; + sh:path biolink:max_research_phase ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_supporting_studies ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ] ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; + sh:property [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:has_quotient ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:frequency_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:has_percentage ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:object_direction_qualifier ], + sh:order 10 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:qualified_predicate ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 6 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:has_percentage ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 12 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:has_total ], + sh:order 7 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 13 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:subject_aspect_qualifier ] ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:object_aspect_qualifier ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . biolink:EnvironmentalExposure a sh:NodeShape ; sh:closed true ; sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -11447,45 +11415,56 @@ biolink:EnvironmentalExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ] ; - sh:targetClass biolink:EnvironmentalExposure . - -biolink:EnvironmentalFeature a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 9 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 11 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:EnvironmentalExposure . + +biolink:EnvironmentalFeature a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -11493,210 +11472,231 @@ biolink:EnvironmentalFeature a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ] ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ] ; sh:targetClass biolink:EnvironmentalFeature . biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:is_toxic ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ] ; + sh:path biolink:id ] ; sh:targetClass biolink:EnvironmentalFoodContaminant . biolink:EnvironmentalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ] ; + sh:path biolink:category ] ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; @@ -11721,28 +11721,22 @@ biolink:Event a sh:NodeShape ; sh:description "Something that happens at a given place and time." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; @@ -11759,28 +11753,34 @@ biolink:Event a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -11793,55 +11793,47 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:closed true ; sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -11853,59 +11845,39 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Exon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Transcript ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -11913,74 +11885,52 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -11988,182 +11938,101 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:ExonToTranscriptRelationship . - -biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an exposure event and an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 32 ; + sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:NamedThing ; + [ sh:class biolink:Exon ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 14 ; + sh:path biolink:original_subject ] ; + sh:targetClass biolink:ExonToTranscriptRelationship . + +biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between an exposure event and an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -12171,11 +12040,22 @@ biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:order 26 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -12183,156 +12063,81 @@ biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:order 16 ; sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:time ; - sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:population_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ] ; - sh:targetClass biolink:ExposureEventToOutcomeAssociation . - -biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:ExposureEvent ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:order 2 ; sh:path rdf:subject ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -12344,90 +12149,31 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], + sh:order 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -12435,115 +12181,215 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 10 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 30 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:population_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 33 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:ExposureEventToOutcomeAssociation . + +biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:iri ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 42 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], + sh:order 30 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:double ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 33 ; + sh:path biolink:id ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; @@ -12554,215 +12400,363 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 32 ; - sh:path biolink:has_supporting_studies ] ; - sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . - -biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; - sh:closed false ; - sh:description "Qualifiers for disease or phenotype to entity associations." ; - sh:ignoredProperties ( biolink:sex_qualifier biolink:has_count biolink:has_total biolink:has_quotient rdf:type biolink:has_percentage ) ; - sh:property [ sh:datatype ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 50 ; sh:path biolink:frequency_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 48 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ] ; - sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . - -biolink:Food a sh:NodeShape ; - sh:closed true ; - sh:description "A substance consumed by a living organism as a source of nutrition" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 37 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + sh:order 49 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . + +biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; + sh:closed false ; + sh:description "Qualifiers for disease or phenotype to entity associations." ; + sh:ignoredProperties ( biolink:has_quotient biolink:sex_qualifier biolink:has_count biolink:has_total rdf:type biolink:has_percentage ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ] ; + sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . + +biolink:Food a sh:NodeShape ; + sh:closed true ; + sh:description "A substance consumed by a living organism as a source of nutrition" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ] ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ] ; sh:targetClass biolink:Food . biolink:FoodAdditive a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -12770,67 +12764,73 @@ biolink:FoodAdditive a sh:NodeShape ; sh:order 13 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:boolean ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:is_toxic ], + sh:order 0 ; + sh:path biolink:trade_name ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path dct:description ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 1 ; @@ -12840,34 +12840,34 @@ biolink:FoodAdditive a sh:NodeShape ; biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifier for frequency type associations" ; - sh:ignoredProperties ( biolink:sex_qualifier biolink:has_count biolink:subject_direction_qualifier biolink:has_total biolink:object_direction_qualifier biolink:has_quotient rdf:type biolink:qualified_predicate biolink:disease_context_qualifier biolink:object_aspect_qualifier biolink:subject_aspect_qualifier biolink:has_percentage ) ; - sh:property [ sh:datatype xsd:string ; + sh:ignoredProperties ( biolink:object_aspect_qualifier biolink:has_percentage biolink:subject_direction_qualifier biolink:has_quotient biolink:sex_qualifier biolink:object_direction_qualifier biolink:subject_aspect_qualifier biolink:has_count biolink:qualified_predicate biolink:disease_context_qualifier rdf:type biolink:has_total ) ; + sh:property [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:frequency_qualifier ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 1 ; + sh:path rdf:subject ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ] ; + sh:order 3 ; + sh:path rdf:object ] ; sh:targetClass biolink:FrequencyQualifierMixin . biolink:FrequencyQuantifier a sh:NodeShape ; @@ -12902,123 +12902,109 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; @@ -13026,71 +13012,79 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; @@ -13103,52 +13097,52 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ] ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:FunctionalAssociation . biolink:Fungus a sh:NodeShape ; sh:closed true ; sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -13159,17 +13153,21 @@ biolink:Fungus a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -13177,17 +13175,24 @@ biolink:Fungus a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -13199,16 +13204,11 @@ biolink:Fungus a sh:NodeShape ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Fungus . biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; @@ -13216,102 +13216,254 @@ biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:original_subject ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 31 ; + sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 22 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:object_category ], + sh:order 18 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 26 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 43 ; - sh:path biolink:retrieval_source_ids ], + sh:order 15 ; + sh:path biolink:species_context_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 46 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:timepoint ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_derivative_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:original_object ], + sh:order 39 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 54 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:id ], [ sh:class biolink:AnatomicalEntity ; sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:anatomical_context_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:knowledge_level ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:qualified_predicate ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:knowledge_source ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 43 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:object_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 48 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 53 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 16 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 46 ; - sh:path biolink:has_supporting_studies ], + sh:order 21 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 52 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -13324,273 +13476,205 @@ biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 28 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:p_value ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 16 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:object_category ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:negated ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 53 ; - sh:path biolink:has_attribute ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:object_closure ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:order 25 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:GeneAffectsChemicalAssociation . + +biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:qualifier ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:subject_category ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:subject_label_closure ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 54 ; + sh:order 42 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:species_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:category ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:predicate ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path rdf:object ], + sh:order 40 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 9 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:object_category_closure ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 46 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:id ] ; - sh:targetClass biolink:GeneAffectsChemicalAssociation . - -biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:order 43 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 41 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -13598,256 +13682,172 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:double ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 44 ; + sh:path biolink:has_total ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 37 ; + sh:path biolink:category ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 45 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ] ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:disease_context_qualifier ] ; sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . biolink:GeneExpressionMixin a sh:NodeShape ; sh:closed false ; sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:class biolink:LifeStage ; + sh:property [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:stage_qualifier ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], [ sh:class biolink:OntologyClass ; sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:quantifier_qualifier ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ] ; + sh:order 1 ; + sh:path biolink:expression_site ] ; sh:targetClass biolink:GeneExpressionMixin . biolink:GeneGroupingMixin a sh:NodeShape ; @@ -13864,58 +13864,109 @@ biolink:GeneGroupingMixin a sh:NodeShape ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:object_namespace ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path biolink:qualified_predicate ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:has_percentage ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; @@ -13923,68 +13974,35 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_count ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], + sh:order 6 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 36 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 17 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -13992,118 +14010,94 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 46 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 44 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 47 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:timepoint ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:original_object ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 41 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -14111,56 +14105,62 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:order 40 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 49 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ] ; + sh:order 22 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . biolink:GeneProductIsoformMixin a sh:NodeShape ; @@ -14189,145 +14189,52 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -14336,272 +14243,234 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:order 5 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 6 ; + sh:path rdf:object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 41 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ] ; - sh:targetClass biolink:GeneRegulatesGeneAssociation . - -biolink:GeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type biolink:subject_form_or_variant_qualifier ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 2 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:double ; + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 34 ; sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 39 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 15 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:GeneRegulatesGeneAssociation . + +biolink:GeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( biolink:subject_form_or_variant_qualifier rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:disease_context_qualifier ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; sh:maxCount 1 ; @@ -14609,311 +14478,454 @@ biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 38 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 36 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path biolink:has_percentage ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ] ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:GeneToDiseaseAssociation . biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; - sh:ignoredProperties ( rdf:type biolink:subject_form_or_variant_qualifier ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:ignoredProperties ( biolink:subject_form_or_variant_qualifier rdf:type ) ; + sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 44 ; + sh:path biolink:has_total ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], + sh:order 43 ; + sh:path biolink:has_count ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:double ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; @@ -14923,63 +14935,75 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 45 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 46 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:object_aspect_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; + sh:order 40 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -14987,48 +15011,24 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 36 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ] ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:disease_context_qualifier ] ; sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . biolink:GeneToEntityAssociationMixin a sh:NodeShape ; @@ -15061,111 +15061,150 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "expression relationship" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], [ sh:class biolink:LifeStage ; sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:stage_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "can be used to indicate magnitude, or also ranking" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:quantifier_qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -15173,274 +15212,196 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:order 20 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:GeneToExpressionSiteAssociation . biolink:GeneToGeneAssociation a sh:NodeShape ; sh:closed false ; sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; - sh:ignoredProperties ( rdf:type biolink:stage_qualifier biolink:expression_site biolink:interacting_molecules_category biolink:phenotypic_state biolink:quantifier_qualifier ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; + sh:ignoredProperties ( biolink:expression_site biolink:quantifier_qualifier biolink:interacting_molecules_category biolink:stage_qualifier biolink:phenotypic_state rdf:type ) ; + sh:property [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -15449,71 +15410,109 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -15521,10 +15520,11 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; + sh:order 16 ; + sh:path biolink:original_object ] ; sh:targetClass biolink:GeneToGeneAssociation . biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; @@ -15537,35 +15537,22 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -15573,13 +15560,23 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:id ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; @@ -15591,19 +15588,45 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -15611,44 +15634,17 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 40 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 36 ; + sh:path biolink:iri ], [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; @@ -15656,415 +15652,235 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:order 2 ; sh:path biolink:stage_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ] ; - sh:targetClass biolink:GeneToGeneCoexpressionAssociation . - -biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 5 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 39 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; + sh:order 34 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 15 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "membership of the gene in the given gene family." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; - sh:path biolink:iri ], + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:object_namespace ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 38 ; sh:path rdf:type ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 8 ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:GeneToGeneCoexpressionAssociation . + +biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:GeneToGeneFamilyAssociation . - -biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "membership of the gene in the given gene family." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -16072,34 +15888,32 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "homology relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -16107,158 +15921,181 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:GeneFamily ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; + sh:order 14 ; + sh:path biolink:original_subject ] ; + sh:targetClass biolink:GeneToGeneFamilyAssociation . + +biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:GeneToGeneHomologyAssociation . - -biolink:GeneToGeneProductRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A gene is transcribed and potentially translated to a gene product" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -16266,56 +16103,58 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:order 24 ; sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:GeneProductMixin ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; @@ -16327,17 +16166,59 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "homology relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -16346,31 +16227,73 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:order 31 ; sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:GeneToGeneHomologyAssociation . + +biolink:GeneToGeneProductRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is transcribed and potentially translated to a gene product" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -16378,191 +16301,226 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:GeneToGeneProductRelationship . - -biolink:GeneToGoTermAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:GeneProductMixin ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 35 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneToGeneProductRelationship . + +biolink:GeneToGoTermAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -16570,117 +16528,182 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:GeneToGoTermAssociation . + +biolink:GeneToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a gene or gene product and a biological process or pathway." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -16688,133 +16711,184 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:GeneToGoTermAssociation . - -biolink:GeneToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a gene or gene product and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -16827,125 +16901,85 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:GeneToPathwayAssociation . + +biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 16 ; - sh:path biolink:original_object ], + sh:path biolink:agent_type ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 7 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:GeneToPathwayAssociation . - -biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 46 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -16957,191 +16991,157 @@ biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 44 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 48 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 6 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 43 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 40 ; + sh:path dct:description ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -17150,32 +17150,39 @@ biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 39 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; @@ -17183,65 +17190,51 @@ biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ] ; + sh:order 24 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . biolink:Genome a sh:NodeShape ; sh:closed true ; sh:description "A genome is the sum of genetic material within a cell or virion." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -17249,26 +17242,39 @@ biolink:Genome a sh:NodeShape ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -17281,28 +17287,22 @@ biolink:Genome a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -17314,119 +17314,119 @@ biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:closed true ; sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_gene_or_gene_product ], + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 8 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 2 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path dct:description ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 8 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:xref ] ; + sh:order 14 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; @@ -17445,16 +17445,27 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], + sh:order 43 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -17466,59 +17477,85 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 1 ; + sh:path biolink:end_interbase_coordinate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; + sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], + sh:order 3 ; + sh:path biolink:strand ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:start_interbase_coordinate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:end_interbase_coordinate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], + sh:order 12 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -17530,62 +17567,96 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], + sh:order 6 ; + sh:path rdf:predicate ], + [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; + sh:in ( "+" "-" "." "?" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:genome_build ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:phase ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 41 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:order 8 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:class biolink:NucleicAcidEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -17593,118 +17664,58 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:genome_build ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], + sh:order 20 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path rdfs:label ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:id ], - [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:strand ] ; + sh:order 28 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:GenomicSequenceLocalization . biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -17712,51 +17723,86 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -17764,295 +17810,209 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; @@ -18061,176 +18021,209 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 44 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that genotype" ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ] ; sh:targetClass biolink:GenotypeToDiseaseAssociation . biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -18243,69 +18236,86 @@ biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:GenotypeToEntityAssociationMixin . biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -18314,106 +18324,95 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:Gene ; sh:description "gene implicated in genotype" ; sh:maxCount 1 ; @@ -18421,87 +18420,76 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "the relationship type used to connect genotype to gene" ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:GenotypeToGeneAssociation . biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Genotype ; sh:description "child genotype" ; sh:maxCount 1 ; @@ -18509,54 +18497,23 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -18565,121 +18522,150 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -18687,21 +18673,35 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ] ; + sh:order 7 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:GenotypeToGenotypePartAssociation . biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -18709,137 +18709,199 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 48 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path dct:description ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], + sh:order 43 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_percentage ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -18847,59 +18909,33 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 5 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -18907,419 +18943,383 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 40 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], + sh:order 42 ; + sh:path biolink:has_total ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ] ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:subject_aspect_qualifier ] ; sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "the relationship type used to connect genotype to gene" ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:GenotypicSex . biolink:GeographicExposure a sh:NodeShape ; @@ -19327,27 +19327,45 @@ biolink:GeographicExposure a sh:NodeShape ; sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -19355,17 +19373,27 @@ biolink:GeographicExposure a sh:NodeShape ; sh:order 4 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -19373,182 +19401,125 @@ biolink:GeographicExposure a sh:NodeShape ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:order 13 ; + sh:path dct:description ] ; + sh:targetClass biolink:GeographicExposure . + +biolink:GeographicLocation a sh:NodeShape ; + sh:closed true ; + sh:description "a location that can be described in lat/long coordinates" ; + sh:ignoredProperties ( rdf:type biolink:timepoint ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ] ; - sh:targetClass biolink:GeographicExposure . - -biolink:GeographicLocation a sh:NodeShape ; - sh:closed true ; - sh:description "a location that can be described in lat/long coordinates" ; - sh:ignoredProperties ( biolink:timepoint rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:latitude ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:float ; + sh:description "longitude" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 1 ; + sh:path biolink:longitude ], + [ sh:datatype xsd:float ; + sh:description "latitude" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:latitude ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:longitude ] ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:GeographicLocation . biolink:GeographicLocationAtTime a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates, for a particular time" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:latitude ], [ sh:datatype xsd:float ; sh:description "longitude" ; sh:maxCount 1 ; @@ -19556,60 +19527,98 @@ biolink:GeographicLocationAtTime a sh:NodeShape ; sh:order 2 ; sh:path biolink:longitude ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "latitude" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:latitude ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ] ; + sh:order 11 ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -19621,112 +19630,64 @@ biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:GrossAnatomicalStructure . - -biolink:Haplotype a sh:NodeShape ; - sh:closed true ; - sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path rdfs:label ], + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:order 6 ; + sh:path biolink:id ] ; + sh:targetClass biolink:GrossAnatomicalStructure . + +biolink:Haplotype a sh:NodeShape ; + sh:closed true ; + sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -19740,20 +19701,37 @@ biolink:Haplotype a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -19761,53 +19739,83 @@ biolink:Haplotype a sh:NodeShape ; sh:order 3 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:Haplotype . - -biolink:Hospitalization a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 13 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 11 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:Haplotype . + +biolink:Hospitalization a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -19820,24 +19828,16 @@ biolink:Hospitalization a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; + sh:order 3 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -19850,23 +19850,34 @@ biolink:Human a sh:NodeShape ; sh:closed true ; sh:description "A member of the the species Homo sapiens." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -19874,17 +19885,26 @@ biolink:Human a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -19898,31 +19918,11 @@ biolink:Human a sh:NodeShape ; sh:order 1 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -19934,19 +19934,19 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:closed true ; sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -19954,18 +19954,33 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -19973,10 +19988,39 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -19984,76 +20028,46 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -20062,128 +20076,108 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ] ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ] ; sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . biolink:Invertebrate a sh:NodeShape ; sh:closed true ; sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -20191,83 +20185,74 @@ biolink:Invertebrate a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Invertebrate . biolink:JournalArticle a sh:NodeShape ; sh:closed true ; sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:volume ], [ sh:datatype xsd:anyURI ; sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; @@ -20275,18 +20260,34 @@ biolink:JournalArticle a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:published_in ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:issue ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:creation_date ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; @@ -20294,44 +20295,38 @@ biolink:JournalArticle a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], + sh:order 25 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 8 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; @@ -20341,51 +20336,56 @@ biolink:JournalArticle a sh:NodeShape ; [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:license ], + sh:order 12 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:pages ], + sh:order 19 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:keywords ], + sh:order 21 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:format ], + sh:order 22 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:volume ], + sh:order 13 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:iso_abbreviation ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:rights ], + sh:order 5 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; @@ -20406,22 +20406,36 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -20429,9 +20443,10 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:order 12 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -20443,32 +20458,6 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -20476,100 +20465,111 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:order 6 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:in_taxon_label ] ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ] ; sh:targetClass biolink:MacromolecularComplex . biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; @@ -20577,457 +20577,457 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:BiologicalProcess ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:BiologicalProcess ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:CellularComponent ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:class biolink:CellularComponent ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ] ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ] ; sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; @@ -21042,70 +21042,82 @@ biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -21113,69 +21125,66 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -21183,107 +21192,98 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ] ; + sh:order 16 ; + sh:path biolink:original_object ] ; sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . biolink:Mammal a sh:NodeShape ; @@ -21296,6 +21296,12 @@ biolink:Mammal a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -21310,58 +21316,52 @@ biolink:Mammal a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -21386,149 +21386,156 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "derivation relationship" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:NamedThing ; + sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -21536,268 +21543,263 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "derivation relationship" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; + sh:order 28 ; + sh:path biolink:p_value ] ; sh:targetClass biolink:MaterialSampleDerivationAssociation . biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and a disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -21805,13 +21807,12 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -21819,31 +21820,37 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between a material sample and something." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -21856,97 +21863,90 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:predicate ] ; sh:targetClass biolink:MaterialSampleToEntityAssociationMixin . biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; @@ -21980,51 +21980,77 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -22032,152 +22058,115 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:order 38 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -22185,97 +22174,193 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ] ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22283,12 +22368,6 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -22300,240 +22379,204 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ] ; + sh:order 31 ; + sh:path biolink:id ] ; sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -22541,56 +22584,56 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22599,11 +22642,12 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Pathway ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22611,90 +22655,39 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ] ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:MolecularActivityToPathwayAssociation . biolink:MolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -22702,16 +22695,32 @@ biolink:MolecularMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:id ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; @@ -22719,68 +22728,59 @@ biolink:MolecularMixture a sh:NodeShape ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdf:type ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ] ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -22793,63 +22793,12 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:population_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], + sh:order 16 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -22857,26 +22806,50 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:order 41 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:subject_context_qualifier ], + sh:order 42 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -22884,50 +22857,29 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:order 20 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:order 7 ; + sh:path biolink:population_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:timepoint ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -22935,17 +22887,21 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:order 17 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path rdfs:label ], + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -22954,18 +22910,12 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:order 3 ; sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -22973,95 +22923,133 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], + sh:order 21 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:deprecated ], + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ] ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ] ; sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . biolink:NoncodingRNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -23069,64 +23057,76 @@ biolink:NoncodingRNAProduct a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; @@ -23140,11 +23140,6 @@ biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -23152,48 +23147,36 @@ biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -23201,77 +23184,93 @@ biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:NucleicAcidSequenceMotif . biolink:NucleosomeModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -23291,16 +23290,17 @@ biolink:NucleosomeModification a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ] ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; @@ -23308,33 +23308,42 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -23344,18 +23353,6 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -23363,38 +23360,41 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 8 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ] ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; @@ -23407,75 +23407,74 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:closed true ; sh:description "describes a characteristic of an organismal entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -23483,28 +23482,29 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:OrganismAttribute . biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:closed false ; sh:description "An association between an organism taxon and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -23512,75 +23512,60 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:OrganismTaxonToEntityAssociation . biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "the environment in which the organism occurs" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -23589,114 +23574,50 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "the environment in which the organism occurs" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; @@ -23704,827 +23625,719 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ] ; - sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . - -biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "A relationship between two organism taxon nodes" ; - sh:ignoredProperties ( rdf:type biolink:associated_environmental_context ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . + +biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "A relationship between two organism taxon nodes" ; + sh:ignoredProperties ( biolink:associated_environmental_context rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . - -biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; + sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 20 ; sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . + +biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "the environment in which the two taxa interact" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], + sh:order 36 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . - -biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; - sh:closed true ; - sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 0 ; + sh:path biolink:associated_environmental_context ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; + sh:order 26 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 9 ; sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 2 ; sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 4 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . + sh:order 22 ; + sh:path biolink:subject_category_closure ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . -biolink:OrganismToOrganismAssociation a sh:NodeShape ; +biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:closed true ; + sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:IndividualOrganism ; - sh:description "An association between two individual organisms." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -24532,29 +24345,19 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -24562,71 +24365,151 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . + +biolink:OrganismToOrganismAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:IndividualOrganism ; + sh:description "An association between two individual organisms." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -24634,254 +24517,323 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:OrganismToOrganismAssociation . - -biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:IndividualOrganism ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:OrganismToOrganismAssociation . + +biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OrganismalEntity ; sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; sh:maxCount 1 ; @@ -24890,209 +24842,218 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . - -biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; - sh:ignoredProperties ( biolink:interacting_molecules_category rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:original_object ] ; + sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + +biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; + sh:ignoredProperties ( rdf:type biolink:interacting_molecules_category ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "interaction relationship type" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -25100,26 +25061,6 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; @@ -25131,45 +25072,135 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ] ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ] ; sh:targetClass biolink:PairwiseGeneToGeneInteraction . biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction at the molecular level between two physical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "interaction relationship type" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -25177,16 +25208,35 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:order 19 ; sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:MolecularEntity ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:MolecularEntity ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -25201,237 +25251,190 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "interaction relationship type" ; + sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 32 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:MolecularEntity ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ] ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ] ; sh:targetClass biolink:PairwiseMolecularInteraction . biolink:Patent a sh:NodeShape ; sh:closed true ; sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:property [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -25439,86 +25442,83 @@ biolink:Patent a sh:NodeShape ; sh:order 16 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 18 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ] ; + sh:path biolink:pages ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -25531,81 +25531,70 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:closed true ; sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 12 ; @@ -25617,11 +25606,22 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:order 4 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ] ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; @@ -25635,53 +25635,17 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -25690,28 +25654,64 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:PathologicalAnatomicalStructure . biolink:PathologicalEntityMixin a sh:NodeShape ; @@ -25724,99 +25724,99 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ] ; + sh:order 16 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:PathologicalProcess . biolink:PathologicalProcessExposure a sh:NodeShape ; @@ -25829,68 +25829,63 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:full_name ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -25898,22 +25893,27 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ] ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -25930,267 +25930,304 @@ biolink:Phenomenon a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Phenomenon . biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:property [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 45 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_namespace ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdf:type ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_percentage ], + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -26198,140 +26235,112 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ] ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ] ; sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:predicate ], - [ sh:class biolink:PhenotypicFeature ; + sh:property [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path rdf:subject ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:frequency_qualifier ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_total ], + sh:order 5 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:subject_direction_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_total ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -26339,174 +26348,190 @@ biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path rdf:object ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:double ; + sh:order 12 ; + sh:path rdf:predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_direction_qualifier ], + sh:order 10 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ] ; + sh:order 4 ; + sh:path biolink:has_percentage ] ; sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; @@ -26520,157 +26545,132 @@ biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 37 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 45 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 8 ; + sh:path biolink:publications ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path biolink:frequency_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], + sh:order 24 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], + sh:order 36 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ] ; + sh:order 28 ; + sh:path biolink:object_label_closure ] ; sh:targetClass biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . biolink:PhenotypicQuality a sh:NodeShape ; @@ -26678,39 +26678,22 @@ biolink:PhenotypicQuality a sh:NodeShape ; sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -26722,74 +26705,91 @@ biolink:PhenotypicQuality a sh:NodeShape ; sh:order 7 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ] ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:PhenotypicQuality . biolink:PhenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -26798,16 +26798,17 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:order 5 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -26816,43 +26817,42 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:order 1 ; sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; @@ -26870,22 +26870,40 @@ biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 12 ; @@ -26896,90 +26914,81 @@ biolink:PhysiologicalProcess a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:order 11 ; + sh:path biolink:category ] ; sh:targetClass biolink:PhysiologicalProcess . biolink:PlanetaryEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists at the level of the whole planet" ; - sh:ignoredProperties ( biolink:timepoint rdf:type biolink:longitude biolink:latitude ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:ignoredProperties ( biolink:latitude biolink:longitude rdf:type biolink:timepoint ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -26987,12 +26996,6 @@ biolink:PlanetaryEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -27000,42 +27003,39 @@ biolink:PlanetaryEntity a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; @@ -27043,122 +27043,67 @@ biolink:Plant a sh:NodeShape ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Plant . - -biolink:Polypeptide a sh:NodeShape ; - sh:closed true ; - sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -27171,6 +27116,26 @@ biolink:Polypeptide a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Plant . + +biolink:Polypeptide a sh:NodeShape ; + sh:closed true ; + sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -27181,6 +27146,25 @@ biolink:Polypeptide a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -27188,22 +27172,38 @@ biolink:Polypeptide a sh:NodeShape ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Polypeptide . biolink:PopulationToPopulationAssociation a sh:NodeShape ; @@ -27211,57 +27211,61 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:description "An association between a two populations" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the object of the association" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -27269,38 +27273,42 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that form the subject of the association" ; sh:maxCount 1 ; @@ -27313,56 +27321,63 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -27371,88 +27386,75 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the object of the association" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 17 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:PopulationToPopulationAssociation . biolink:PosttranslationalModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -27460,23 +27462,27 @@ biolink:PosttranslationalModification a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -27484,210 +27490,215 @@ biolink:PosttranslationalModification a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:PosttranslationalModification . biolink:PreprintPublication a sh:NodeShape ; sh:closed true ; sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 18 ; + sh:path rdfs:label ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ] ; sh:targetClass biolink:PreprintPublication . biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:BiologicalProcess ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -27695,113 +27706,80 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -27809,17 +27787,11 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:BiologicalProcess ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -27827,18 +27799,51 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; @@ -27846,27 +27851,22 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -27878,97 +27878,58 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], + sh:order 13 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:is_supplement ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:order 14 ; + sh:path biolink:iri ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:order 17 ; + sh:path rdfs:label ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -27981,34 +27942,82 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ] ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ] ; sh:targetClass biolink:ProcessedMaterial . biolink:Protein a sh:NodeShape ; sh:closed true ; sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -28016,36 +28025,33 @@ biolink:Protein a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -28053,11 +28059,11 @@ biolink:Protein a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -28065,78 +28071,46 @@ biolink:Protein a sh:NodeShape ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ] ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Protein . biolink:ProteinDomain a sh:NodeShape ; sh:closed true ; sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -28144,54 +28118,43 @@ biolink:ProteinDomain a sh:NodeShape ; sh:order 8 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:category ] ; - sh:targetClass biolink:ProteinDomain . - -biolink:ProteinFamily a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; @@ -28201,13 +28164,45 @@ biolink:ProteinFamily a sh:NodeShape ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; - sh:path biolink:has_attribute ], + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:ProteinDomain . + +biolink:ProteinFamily a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -28215,82 +28210,77 @@ biolink:ProteinFamily a sh:NodeShape ; sh:order 8 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ] ; + sh:order 7 ; + sh:path biolink:id ] ; sh:targetClass biolink:ProteinFamily . biolink:ProteinIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -28302,36 +28292,46 @@ biolink:ProteinIsoform a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -28342,17 +28342,30 @@ biolink:ProteinIsoform a sh:NodeShape ; biolink:RNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -28365,95 +28378,76 @@ biolink:RNAProduct a sh:NodeShape ; sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:RNAProduct . - -biolink:RNAProductIsoform a sh:NodeShape ; - sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:RNAProduct . + +biolink:RNAProductIsoform a sh:NodeShape ; + sh:closed true ; + sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -28465,51 +28459,116 @@ biolink:RNAProductIsoform a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ], + sh:path biolink:id ] ; + sh:targetClass biolink:RNAProductIsoform . + +biolink:ReactionToCatalystAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 41 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:RNAProductIsoform . - -biolink:ReactionToCatalystAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MolecularEntity ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:MolecularEntity ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -28517,27 +28576,24 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:order 3 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 4 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:order 35 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -28545,174 +28601,77 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 23 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], + sh:order 6 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -28720,171 +28679,161 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:order 26 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 39 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 5 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 28 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], + sh:order 37 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:order 4 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 35 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -28897,173 +28846,219 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:order 22 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_namespace ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:reaction_direction ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ] ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; sh:closed true ; sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -29072,45 +29067,59 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:order 1 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:ReagentTargetedGene . biolink:RegulatoryRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -29118,65 +29127,56 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ] ; + sh:order 5 ; + sh:path biolink:xref ] ; sh:targetClass biolink:RegulatoryRegion . biolink:RelationshipQuantifier a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( biolink:has_count biolink:has_total biolink:has_quotient rdf:type biolink:has_percentage ) ; + sh:ignoredProperties ( biolink:has_quotient biolink:has_count biolink:has_total rdf:type biolink:has_percentage ) ; sh:targetClass biolink:RelationshipQuantifier . biolink:RelationshipType a sh:NodeShape ; @@ -29196,16 +29196,40 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a relative frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -29214,17 +29238,19 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -29238,52 +29264,26 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:order 3 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:RelativeFrequencyAnalysisResult . biolink:SensitivityQuantifier a sh:NodeShape ; @@ -29294,36 +29294,83 @@ biolink:SensitivityQuantifier a sh:NodeShape ; biolink:SequenceAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; - sh:ignoredProperties ( biolink:strand biolink:end_interbase_coordinate rdf:type biolink:start_interbase_coordinate biolink:genome_build biolink:phase ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:ignoredProperties ( biolink:end_interbase_coordinate biolink:phase biolink:start_interbase_coordinate biolink:genome_build biolink:strand rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -29335,23 +29382,28 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -29359,165 +29411,113 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ] ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:SequenceAssociation . biolink:SequenceFeatureRelationship a sh:NodeShape ; @@ -29525,33 +29525,22 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:description "For example, a particular exon is part of a particular transcript or gene" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -29560,356 +29549,309 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; - sh:path biolink:object_category_closure ] ; - sh:targetClass biolink:SequenceFeatureRelationship . - -biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; + sh:targetClass biolink:SequenceFeatureRelationship . + +biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -29917,49 +29859,70 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -29971,11 +29934,48 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; + sh:order 21 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . biolink:Serial a sh:NodeShape ; @@ -29983,32 +29983,49 @@ biolink:Serial a sh:NodeShape ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:provided_by ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -30016,15 +30033,10 @@ biolink:Serial a sh:NodeShape ; sh:order 13 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:mesh_terms ], + sh:order 12 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; @@ -30033,94 +30045,82 @@ biolink:Serial a sh:NodeShape ; sh:order 17 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:issue ], + sh:order 6 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:summary ], + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], + sh:order 4 ; + sh:path biolink:pages ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 21 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], + sh:order 18 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:volume ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:keywords ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], + sh:order 0 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:pages ], + sh:order 1 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:synonym ], + sh:order 14 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ] ; + sh:order 2 ; + sh:path biolink:issue ] ; sh:targetClass biolink:Serial . biolink:SeverityValue a sh:NodeShape ; @@ -30128,25 +30128,24 @@ biolink:SeverityValue a sh:NodeShape ; sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -30160,30 +30159,21 @@ biolink:SeverityValue a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -30191,38 +30181,55 @@ biolink:SeverityValue a sh:NodeShape ; sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ] ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:SeverityValue . biolink:SiRNA a sh:NodeShape ; sh:closed true ; sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -30235,37 +30242,21 @@ biolink:SiRNA a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -30278,91 +30269,92 @@ biolink:SiRNA a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; sh:closed true ; sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 2 ; sh:path biolink:available_from ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:trade_name ], + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; @@ -30374,15 +30366,29 @@ biolink:SmallMolecule a sh:NodeShape ; sh:order 13 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30395,13 +30401,7 @@ biolink:SmallMolecule a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:SmallMolecule . biolink:Snv a sh:NodeShape ; @@ -30409,65 +30409,34 @@ biolink:Snv a sh:NodeShape ; sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -30496,86 +30465,117 @@ biolink:Snv a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Snv . biolink:SocioeconomicExposure a sh:NodeShape ; sh:closed true ; sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:class biolink:SocioeconomicAttribute ; - sh:description "connects any entity to an attribute" ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:SocioeconomicAttribute ; + sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30618,78 +30618,78 @@ biolink:StudyPopulation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:order 13 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:StudyPopulation . biolink:StudyResult a sh:NodeShape ; @@ -30697,82 +30697,69 @@ biolink:StudyResult a sh:NodeShape ; sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -30780,10 +30767,23 @@ biolink:StudyResult a sh:NodeShape ; sh:order 6 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:StudyResult . biolink:StudyVariable a sh:NodeShape ; @@ -30791,93 +30791,93 @@ biolink:StudyVariable a sh:NodeShape ; sh:description "a variable that is used as a measure in the investigation of a study" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:order 8 ; + sh:path biolink:id ] ; sh:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; @@ -30889,100 +30889,91 @@ biolink:SubjectOfInvestigation a sh:NodeShape ; biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30991,80 +30982,78 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -31073,99 +31062,103 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:TaxonToTaxonAssociation . biolink:TextMiningResult a sh:NodeShape ; sh:closed true ; sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -31173,206 +31166,188 @@ biolink:TextMiningResult a sh:NodeShape ; sh:order 6 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:TextMiningResult . - -biolink:ThingWithTaxon a sh:NodeShape ; - sh:closed false ; - sh:description "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:ThingWithTaxon . - -biolink:TranscriptToGeneRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A gene is a collection of transcripts" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 12 ; - sh:path biolink:agent_type ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 8 ; + sh:path biolink:id ] ; + sh:targetClass biolink:TextMiningResult . + +biolink:ThingWithTaxon a sh:NodeShape ; + sh:closed false ; + sh:description "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:ThingWithTaxon . + +biolink:TranscriptToGeneRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is a collection of transcripts" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -31384,74 +31359,99 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Transcript ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ] ; + sh:order 28 ; + sh:path biolink:p_value ] ; sh:targetClass biolink:TranscriptToGeneRelationship . biolink:TranscriptionFactorBindingSite a sh:NodeShape ; @@ -31459,11 +31459,17 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -31471,28 +31477,17 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -31505,83 +31500,86 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:order 2 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ] ; + sh:order 8 ; + sh:path biolink:iri ] ; sh:targetClass biolink:TranscriptionFactorBindingSite . biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; @@ -31589,22 +31587,33 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 41 ; sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -31612,460 +31621,451 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 36 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ] ; + sh:order 8 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "E.g. is pathogenic for" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ] ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ] ; sh:targetClass biolink:VariantToDiseaseAssociation . biolink:VariantToEntityAssociationMixin a sh:NodeShape ; @@ -32097,43 +32097,135 @@ biolink:VariantToEntityAssociationMixin a sh:NodeShape ; biolink:VariantToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; - sh:ignoredProperties ( rdf:type biolink:stage_qualifier biolink:expression_site biolink:phenotypic_state biolink:quantifier_qualifier ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:ignoredProperties ( biolink:expression_site biolink:quantifier_qualifier biolink:stage_qualifier biolink:phenotypic_state rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -32146,555 +32238,406 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 31 ; + sh:path biolink:id ] ; + sh:targetClass biolink:VariantToGeneAssociation . + +biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:order 4 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:VariantToGeneAssociation . - -biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:order 40 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:phenotypic_state ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 34 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:order 35 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:original_object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 2 ; + sh:path biolink:stage_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 36 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path rdf:predicate ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:VariantToGeneExpressionAssociation . - -biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 39 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:VariantToGeneExpressionAssociation . + +biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 38 ; + sh:path dct:description ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 45 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -32702,113 +32645,178 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 36 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 43 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 26 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 49 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -32821,45 +32829,23 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], + sh:order 48 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -32867,113 +32853,158 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 16 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ] ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:timepoint ], + sh:order 39 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], + sh:order 41 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 11 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that is observed to have the frequency" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "number all populations that carry a particular allele, aka allele number" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 4 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 6 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:deprecated ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:has_percentage ], + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:SequenceVariant ; sh:description "an allele that has a certain frequency in a given population" ; sh:maxCount 1 ; @@ -32981,155 +33012,124 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "number all populations that carry a particular allele, aka allele number" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_total ], + sh:order 37 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:double ; + sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:order 5 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_count ], + sh:order 8 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], + sh:order 36 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that is observed to have the frequency" ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:integer ; + sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_count ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:double ; - sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ] ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:VariantToPopulationAssociation . biolink:Vertebrate a sh:NodeShape ; @@ -33137,77 +33137,77 @@ biolink:Vertebrate a sh:NodeShape ; sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -33220,105 +33220,100 @@ biolink:Virus a sh:NodeShape ; sh:closed true ; sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:Virus . biolink:WebPage a sh:NodeShape ; sh:closed true ; sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:property [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -33326,231 +33321,276 @@ biolink:WebPage a sh:NodeShape ; sh:order 21 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ] ; + sh:order 13 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:WebPage . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:has_input ] ; + sh:path biolink:has_input ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ] ; sh:targetClass biolink:Behavior . biolink:BehavioralFeature a sh:NodeShape ; sh:closed true ; sh:description "A phenotypic feature which is behavioral in nature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; @@ -33561,86 +33601,57 @@ biolink:BehavioralFeature a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:BehavioralFeature . biolink:CellularComponent a sh:NodeShape ; sh:closed true ; sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -33650,98 +33661,90 @@ biolink:CellularComponent a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:CellularComponent . biolink:ClinicalAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -33750,37 +33753,34 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:order 5 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:ClinicalAttribute . biolink:Dataset a sh:NodeShape ; @@ -33788,115 +33788,111 @@ biolink:Dataset a sh:NodeShape ; sh:description "an item that refers to a collection of data from a data source." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:Dataset . biolink:DatasetDistribution a sh:NodeShape ; sh:closed true ; sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -33904,14 +33900,21 @@ biolink:DatasetDistribution a sh:NodeShape ; sh:order 13 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -33925,17 +33928,19 @@ biolink:DatasetDistribution a sh:NodeShape ; sh:order 4 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:rights ], + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:license ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -33948,27 +33953,22 @@ biolink:DatasetDistribution a sh:NodeShape ; sh:order 0 ; sh:path biolink:distribution_download_url ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -33981,39 +33981,49 @@ biolink:Device a sh:NodeShape ; sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34032,43 +34042,53 @@ biolink:Device a sh:NodeShape ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ] ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Device . biolink:Exon a sh:NodeShape ; sh:closed true ; sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -34080,22 +34100,6 @@ biolink:Exon a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -34115,111 +34119,107 @@ biolink:Exon a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ] ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Exon . biolink:GeneFamily a sh:NodeShape ; sh:closed true ; sh:description "any grouping of multiple genes or gene products related by common descent" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ] ; + sh:order 7 ; + sh:path biolink:id ] ; sh:targetClass biolink:GeneFamily . biolink:GeneProductMixin a sh:NodeShape ; @@ -34231,66 +34231,67 @@ biolink:GeneProductMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:GeneProductMixin . biolink:GeneticInheritance a sh:NodeShape ; sh:closed true ; sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34298,159 +34299,134 @@ biolink:GeneticInheritance a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:GeneticInheritance . biolink:InformationContentEntity a sh:NodeShape ; sh:closed false ; sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; - sh:ignoredProperties ( biolink:pages dct:distribution biolink:iso_abbreviation biolink:authors biolink:has_dataset biolink:upstream_resource_ids biolink:volume schema1:logo biolink:keywords biolink:source_web_page biolink:distribution_download_url dct:type biolink:chapter rdf:type biolink:summary biolink:resource_id biolink:published_in biolink:issue biolink:resource_role biolink:mesh_terms biolink:ingest_date ) ; - sh:property [ sh:datatype xsd:string ; + sh:ignoredProperties ( biolink:published_in biolink:upstream_resource_ids biolink:authors biolink:mesh_terms schema1:logo biolink:issue dct:distribution biolink:resource_id biolink:source_web_page biolink:chapter biolink:has_dataset biolink:resource_role biolink:volume biolink:summary biolink:pages biolink:ingest_date biolink:keywords biolink:iso_abbreviation biolink:distribution_download_url dct:type rdf:type ) ; + sh:property [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; - sh:targetClass biolink:InformationContentEntity . - -biolink:Onset a sh:NodeShape ; - sh:closed true ; - sh:description "The age group in which (disease) symptom manifestations appear." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:InformationContentEntity . + +biolink:Onset a sh:NodeShape ; + sh:closed true ; + sh:description "The age group in which (disease) symptom manifestations appear." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; @@ -34460,90 +34436,120 @@ biolink:Onset a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:Onset . biolink:OrganismalEntity a sh:NodeShape ; sh:closed false ; sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34551,15 +34557,16 @@ biolink:OrganismalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -34567,58 +34574,38 @@ biolink:OrganismalEntity a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:OrganismalEntity . biolink:PredicateMapping a sh:NodeShape ; sh:closed true ; sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:object_derivative_qualifier ], + sh:order 18 ; + sh:path biolink:exact_match ], [ sh:datatype xsd:string ; sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; @@ -34626,100 +34613,113 @@ biolink:PredicateMapping a sh:NodeShape ; sh:order 4 ; sh:path biolink:subject_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:mapped_predicate ], [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:object_part_qualifier ], + sh:order 5 ; + sh:path biolink:subject_derivative_qualifier ], [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], + sh:order 20 ; + sh:path biolink:broad_match ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualified_predicate ], + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ], + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:object_context_qualifier ], + sh:order 11 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:narrow_match ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:order 8 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], + sh:order 17 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 7 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:exact_match ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 14 ; + sh:path biolink:object_context_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ] ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:object_part_qualifier ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; @@ -34732,6 +34732,23 @@ biolink:Procedure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -34744,55 +34761,38 @@ biolink:Procedure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ] ; + sh:order 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Procedure . biolink:SocioeconomicAttribute a sh:NodeShape ; @@ -34800,16 +34800,11 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:description "Attributes relating to a socioeconomic manifestation" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -34824,66 +34819,71 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:order 3 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:TaxonomicRank a sh:NodeShape ; @@ -34903,47 +34903,55 @@ biolink:Treatment a sh:NodeShape ; sh:closed true ; sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -34951,136 +34959,128 @@ biolink:Treatment a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:id ], [ sh:class biolink:Drug ; sh:description "connects an entity to one or more drugs" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_drug ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:has_drug ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:timepoint ], [ sh:class biolink:Device ; sh:description "connects an entity to one or more (medical) devices" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_device ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ] ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:Treatment . biolink:Zygosity a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:Zygosity . biolink:Case a sh:NodeShape ; @@ -35088,11 +35088,22 @@ biolink:Case a sh:NodeShape ; sh:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -35100,38 +35111,23 @@ biolink:Case a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -35142,50 +35138,53 @@ biolink:Case a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Case . biolink:CellLine a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -35193,61 +35192,62 @@ biolink:CellLine a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:CellLine . biolink:IndividualOrganism a sh:NodeShape ; @@ -35255,22 +35255,45 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -35278,60 +35301,37 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:IndividualOrganism . biolink:Outcome a sh:NodeShape ; @@ -35345,66 +35345,63 @@ biolink:Transcript a sh:NodeShape ; sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -35416,48 +35413,53 @@ biolink:Transcript a sh:NodeShape ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Transcript . biolink:BiologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -35468,179 +35470,177 @@ biolink:BiologicalProcess a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ] ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:BiologicalProcess . biolink:Drug a sh:NodeShape ; sh:closed true ; sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:is_toxic ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 1 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], + sh:order 5 ; + sh:path biolink:trade_name ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:trade_name ], + sh:order 18 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:is_supplement ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 4 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 14 ; + sh:path biolink:iri ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:Drug . biolink:ExposureEvent a sh:NodeShape ; @@ -35667,37 +35667,45 @@ biolink:MaterialSample a sh:NodeShape ; sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; @@ -35708,124 +35716,116 @@ biolink:MaterialSample a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:MaterialSample . biolink:Pathway a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; @@ -35838,43 +35838,38 @@ biolink:LifeStage a sh:NodeShape ; sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -35887,76 +35882,46 @@ biolink:LifeStage a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ] ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:LifeStage . biolink:NucleicAcidEntity a sh:NodeShape ; sh:closed true ; sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_metabolite ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -35969,87 +35934,131 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 6 ; sh:path biolink:available_from ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:is_metabolite ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ] ; + sh:path biolink:synonym ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:MolecularActivity a sh:NodeShape ; sh:closed true ; sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -36057,17 +36066,38 @@ biolink:MolecularActivity a sh:NodeShape ; sh:order 8 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "The gene product, gene, or complex that catalyzes the reaction" ; sh:nodeKind sh:BlankNodeOrIRI ; @@ -36078,17 +36108,17 @@ biolink:MolecularActivity a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the output for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36096,92 +36126,71 @@ biolink:MolecularActivity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:class biolink:MolecularEntity ; sh:description "A chemical entity that is the input for the reaction" ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:has_input ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the output for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ] ; + sh:path biolink:has_input ] ; sh:targetClass biolink:MolecularActivity . biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:closed true ; sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -36189,17 +36198,11 @@ biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36208,25 +36211,22 @@ biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 13 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . biolink:MacromolecularMachineMixin a sh:NodeShape ; sh:closed false ; sh:description "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; - sh:ignoredProperties ( rdf:type biolink:synonym biolink:xref ) ; + sh:ignoredProperties ( biolink:synonym rdf:type biolink:xref ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -36238,39 +36238,62 @@ biolink:MacromolecularMachineMixin a sh:NodeShape ; biolink:MolecularEntity a sh:NodeShape ; sh:closed true ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; - sh:ignoredProperties ( biolink:in_taxon_label rdf:type biolink:has_biological_sequence biolink:in_taxon ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:ignoredProperties ( biolink:has_biological_sequence biolink:in_taxon_label rdf:type biolink:in_taxon ) ; + sh:property [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_metabolite ], + sh:order 10 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; @@ -36284,18 +36307,15 @@ biolink:MolecularEntity a sh:NodeShape ; sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; @@ -36303,42 +36323,22 @@ biolink:MolecularEntity a sh:NodeShape ; sh:order 4 ; sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:MolecularEntity . biolink:PhysicalEntity a sh:NodeShape ; @@ -36352,38 +36352,31 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -36391,15 +36384,16 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:order 9 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -36407,11 +36401,17 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ] ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PhysicalEntity . biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; @@ -36424,66 +36424,38 @@ biolink:Genotype a sh:NodeShape ; sh:closed true ; sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Zygosity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], + sh:order 1 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -36491,16 +36463,11 @@ biolink:Genotype a sh:NodeShape ; sh:order 4 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36508,27 +36475,54 @@ biolink:Genotype a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Genotype . - -biolink:SequenceVariant a sh:NodeShape ; - sh:closed true ; - sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Zygosity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], + [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:Genotype . + +biolink:SequenceVariant a sh:NodeShape ; + sh:closed true ; + sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -36540,62 +36534,68 @@ biolink:SequenceVariant a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], + sh:order 2 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -36603,23 +36603,28 @@ biolink:SequenceVariant a sh:NodeShape ; sh:order 4 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ] ; + sh:order 9 ; + sh:path biolink:iri ] ; sh:targetClass biolink:SequenceVariant . biolink:ChemicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; - sh:ignoredProperties ( biolink:routes_of_delivery rdf:type biolink:in_taxon biolink:is_supplement biolink:drug_regulatory_status_world_wide biolink:is_metabolite biolink:has_biological_sequence biolink:highest_FDA_approval_status biolink:in_taxon_label ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:ignoredProperties ( biolink:is_metabolite biolink:in_taxon biolink:has_biological_sequence biolink:in_taxon_label biolink:highest_FDA_approval_status biolink:drug_regulatory_status_world_wide biolink:is_supplement biolink:routes_of_delivery rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -36631,38 +36636,44 @@ biolink:ChemicalEntity a sh:NodeShape ; sh:order 12 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:boolean ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:is_toxic ], + sh:order 0 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -36670,44 +36681,33 @@ biolink:ChemicalEntity a sh:NodeShape ; sh:order 7 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ] ; + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ] ; sh:targetClass biolink:ChemicalEntity . biolink:Agent a sh:NodeShape ; @@ -36715,15 +36715,34 @@ biolink:Agent a sh:NodeShape ; sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:affiliation ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -36736,33 +36755,17 @@ biolink:Agent a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:affiliation ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; sh:maxCount 1 ; @@ -36770,39 +36773,42 @@ biolink:Agent a sh:NodeShape ; sh:order 1 ; sh:path biolink:address ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; + sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:Agent . biolink:PhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36815,118 +36821,74 @@ biolink:PhenotypicFeature a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:PhenotypicFeature . biolink:ChemicalRole a sh:NodeShape ; sh:closed true ; sh:description "A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -36938,6 +36900,11 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36945,71 +36912,122 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:ChemicalRole . biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -37023,34 +37041,16 @@ biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeature . biolink:Gene a sh:NodeShape ; @@ -37058,60 +37058,70 @@ biolink:Gene a sh:NodeShape ; sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Symbol for a particular thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:symbol ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; @@ -37119,168 +37129,147 @@ biolink:Gene a sh:NodeShape ; sh:order 2 ; sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ] ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ] ; sh:targetClass biolink:Gene . biolink:BiologicalSex a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; + sh:order 5 ; + sh:path biolink:id ] ; sh:targetClass biolink:BiologicalSex . biolink:AnatomicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A subcellular location, cell type or gross anatomical part" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -37288,45 +37277,56 @@ biolink:AnatomicalEntity a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:AnatomicalEntity . biolink:GeneOrGeneProduct a sh:NodeShape ; sh:closed false ; sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; - sh:ignoredProperties ( rdf:type biolink:synonym biolink:xref ) ; + sh:ignoredProperties ( biolink:synonym rdf:type biolink:xref ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -37357,21 +37357,21 @@ biolink:Disease a sh:NodeShape ; sh:closed true ; sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -37385,20 +37385,38 @@ biolink:Disease a sh:NodeShape ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37411,24 +37429,6 @@ biolink:Disease a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -37441,136 +37441,91 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:closed true ; sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:TaxonomicRank ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_taxonomic_rank ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:category ], - [ sh:class biolink:TaxonomicRank ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_taxonomic_rank ] ; - sh:targetClass biolink:OrganismTaxon . - -biolink:NamedThing a sh:NodeShape ; - sh:closed true ; - sh:description "a databased entity or concept/class" ; - sh:ignoredProperties ( biolink:has_chemical_role biolink:drug_regulatory_status_world_wide biolink:has_quantitative_value biolink:trade_name biolink:iso_abbreviation biolink:address biolink:authors biolink:has_zygosity biolink:enabled_by biolink:has_device biolink:has_input biolink:upstream_resource_ids biolink:has_qualitative_value biolink:is_toxic biolink:is_supplement biolink:has_gene biolink:available_from biolink:has_procedure biolink:distribution_download_url biolink:affiliation biolink:summary biolink:has_biological_sequence biolink:resource_id biolink:has_gene_or_gene_product biolink:has_taxonomic_rank biolink:in_taxon_label biolink:timepoint biolink:published_in biolink:issue biolink:rights biolink:is_metabolite biolink:mesh_terms dct:distribution biolink:symbol biolink:has_attribute_type biolink:has_output biolink:has_dataset biolink:latitude biolink:volume schema1:logo biolink:max_tolerated_dose biolink:format biolink:longitude biolink:creation_date biolink:keywords biolink:source_web_page biolink:highest_FDA_approval_status dct:type biolink:chapter rdf:type biolink:has_drug biolink:resource_role biolink:routes_of_delivery biolink:license biolink:in_taxon biolink:pages biolink:ingest_date ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:synonym ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 9 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 1 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:OrganismTaxon . + +biolink:NamedThing a sh:NodeShape ; + sh:closed true ; + sh:description "a databased entity or concept/class" ; + sh:ignoredProperties ( biolink:creation_date biolink:upstream_resource_ids biolink:authors biolink:trade_name biolink:format biolink:has_output biolink:routes_of_delivery biolink:mesh_terms schema1:logo biolink:has_quantitative_value biolink:issue dct:distribution biolink:has_biological_sequence biolink:in_taxon_label biolink:license biolink:available_from biolink:timepoint biolink:summary biolink:pages biolink:ingest_date biolink:is_metabolite biolink:has_drug biolink:has_gene biolink:symbol biolink:has_procedure biolink:iso_abbreviation biolink:longitude dct:type rdf:type biolink:published_in biolink:has_chemical_role biolink:rights biolink:highest_FDA_approval_status biolink:has_attribute_type biolink:latitude biolink:in_taxon biolink:max_tolerated_dose biolink:has_qualitative_value biolink:is_supplement biolink:resource_id biolink:affiliation biolink:source_web_page biolink:enabled_by biolink:chapter biolink:has_gene_or_gene_product biolink:has_dataset biolink:address biolink:drug_regulatory_status_world_wide biolink:resource_role biolink:volume biolink:has_input biolink:keywords biolink:has_taxonomic_rank biolink:has_device biolink:is_toxic biolink:has_zygosity biolink:distribution_download_url ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -37582,168 +37537,165 @@ biolink:NamedThing a sh:NodeShape ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:NamedThing . - -biolink:EvidenceType a sh:NodeShape ; - sh:closed true ; - sh:description "Class of evidence that supports an association" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:synonym ], + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 0 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:NamedThing . + +biolink:EvidenceType a sh:NodeShape ; + sh:closed true ; + sh:description "Class of evidence that supports an association" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:rights ] ; - sh:targetClass biolink:EvidenceType . - -biolink:Publication a sh:NodeShape ; - sh:closed true ; - sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; - sh:ignoredProperties ( biolink:issue biolink:volume biolink:chapter rdf:type biolink:iso_abbreviation biolink:published_in ) ; - sh:property [ sh:datatype xsd:string ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 2 ; sh:path biolink:format ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:category ] ; + sh:targetClass biolink:EvidenceType . + +biolink:Publication a sh:NodeShape ; + sh:closed true ; + sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; + sh:ignoredProperties ( biolink:published_in biolink:issue biolink:chapter biolink:iso_abbreviation biolink:volume rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; @@ -37754,41 +37706,46 @@ biolink:Publication a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -37800,12 +37757,55 @@ biolink:Publication a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ] ; sh:targetClass biolink:Publication . biolink:RetrievalSource a sh:NodeShape ; @@ -37819,16 +37819,44 @@ biolink:RetrievalSource a sh:NodeShape ; sh:order 18 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:upstream_resource_ids ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:resource_id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -37836,89 +37864,61 @@ biolink:RetrievalSource a sh:NodeShape ; sh:order 13 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:resource_role ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:resource_id ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:upstream_resource_ids ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ] ; + sh:order 5 ; + sh:path biolink:rights ] ; sh:targetClass biolink:RetrievalSource . biolink:Study a sh:NodeShape ; @@ -37926,17 +37926,6 @@ biolink:Study a sh:NodeShape ; sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], @@ -37953,114 +37942,116 @@ biolink:Study a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ] ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Study . biolink:Attribute a sh:NodeShape ; sh:closed true ; sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; - sh:ignoredProperties ( rdf:type biolink:in_taxon biolink:has_biological_sequence biolink:has_gene_or_gene_product biolink:in_taxon_label biolink:timepoint ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; + sh:ignoredProperties ( biolink:in_taxon biolink:has_biological_sequence biolink:in_taxon_label biolink:has_gene_or_gene_product biolink:timepoint rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -38068,27 +38059,36 @@ biolink:Attribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; sh:closed false ; sh:description "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; - sh:ignoredProperties ( biolink:timepoint rdf:type ) ; + sh:ignoredProperties ( rdf:type biolink:timepoint ) ; sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; diff --git a/src/biolink_model/datamodel/model.py b/src/biolink_model/datamodel/model.py index afa3da7f2..ba2e0e7b0 100644 --- a/src/biolink_model/datamodel/model.py +++ b/src/biolink_model/datamodel/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-10-28T20:59:10 +# Generation date: 2024-11-07T15:54:44 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -13888,6 +13888,9 @@ class slots: slots.form_or_variant_qualifier = Slot(uri=BIOLINK.form_or_variant_qualifier, name="form or variant qualifier", curie=BIOLINK.curie('form_or_variant_qualifier'), model_uri=BIOLINK.form_or_variant_qualifier, domain=Association, range=Optional[str]) +slots.specialization_qualifier = Slot(uri=BIOLINK.specialization_qualifier, name="specialization qualifier", curie=BIOLINK.curie('specialization_qualifier'), + model_uri=BIOLINK.specialization_qualifier, domain=Association, range=Optional[str]) + slots.aspect_qualifier = Slot(uri=BIOLINK.aspect_qualifier, name="aspect qualifier", curie=BIOLINK.curie('aspect_qualifier'), model_uri=BIOLINK.aspect_qualifier, domain=Association, range=Optional[str]) @@ -13921,6 +13924,9 @@ class slots: slots.subject_aspect_qualifier = Slot(uri=BIOLINK.subject_aspect_qualifier, name="subject aspect qualifier", curie=BIOLINK.curie('subject_aspect_qualifier'), model_uri=BIOLINK.subject_aspect_qualifier, domain=Association, range=Optional[str]) +slots.subject_specialization_qualifier = Slot(uri=BIOLINK.subject_specialization_qualifier, name="subject specialization qualifier", curie=BIOLINK.curie('subject_specialization_qualifier'), + model_uri=BIOLINK.subject_specialization_qualifier, domain=None, range=Optional[str]) + slots.subject_form_or_variant_qualifier = Slot(uri=BIOLINK.subject_form_or_variant_qualifier, name="subject form or variant qualifier", curie=BIOLINK.curie('subject_form_or_variant_qualifier'), model_uri=BIOLINK.subject_form_or_variant_qualifier, domain=Association, range=Optional[str]) diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml index cbfe24ee4..c84cc8748 100644 --- a/src/biolink_model/schema/biolink_model.yaml +++ b/src/biolink_model/schema/biolink_model.yaml @@ -1316,6 +1316,26 @@ slots: in_subset: - translator_minimal + specialization qualifier: + is_a: qualifier + abstract: true + description: >- + A qualifier that composes with a core subject/object concept to define a more specific version of the + subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept + and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the + subject identifier. + examples: + - value: CHEBI:24431 + description: >- + In a MAXO annotation this would be a specialization in treatment of a disease. For example, + fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent + therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term + 'congenital myasthenic syndrome '4A.' + - value: CL:0000123 + description: >- + In an expression annotation this would be a specialization in location of an anatomical entity. For example, + "expression in the nucleas of hepatic cells" would be a specialization of "expression in hepatic cells" + aspect qualifier: is_a: qualifier abstract: true @@ -1440,6 +1460,14 @@ slots: in_subset: - translator_minimal + subject specialization qualifier: + description: >- + A qualifier that composes with a core subject/object concept to define a more specific version of the + subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept + and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the + subject identifier. + + subject form or variant qualifier: description: >- A qualifier that composes with a core subject/object concept to define a specific type, variant, diff --git a/src/biolink_model/scripts/classprefixes.py b/src/biolink_model/scripts/classprefixes.py index 82d51b794..575551fc1 100644 --- a/src/biolink_model/scripts/classprefixes.py +++ b/src/biolink_model/scripts/classprefixes.py @@ -1,5 +1,5 @@ # Auto generated from class_prefixes.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-10-28T20:59:53 +# Generation date: 2024-11-07T15:55:30 # Schema: BiolinkClassPrefixes # # id: biolink-model-class-prefixes From 2e116b8bb1be0afa5fd981434882e64a623b9170 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 7 Nov 2024 16:13:44 -0800 Subject: [PATCH 2/2] adjust format --- biolink-model.yaml | 20 +- project/graphql/biolink_model.graphql | 48 + project/jsonld/biolink_model.context.jsonld | 7 +- project/jsonld/biolink_model.jsonld | 100 +- project/jsonschema/biolink_model.schema.json | 317 +- project/owl/biolink_model.owl.ttl | 5706 +- project/protobuf/biolink_model.proto | 47 +- project/shacl/biolink_model.shacl.ttl | 43388 ++++++++-------- project/shex/biolink_model.shex | 31 +- src/biolink_model/datamodel/model.py | 129 +- .../datamodel/pydanticmodel_v2.py | 50 +- src/biolink_model/schema/biolink_model.yaml | 27 +- src/biolink_model/scripts/classprefixes.py | 2 +- 13 files changed, 25450 insertions(+), 24422 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index af3f3a5ba..74ae430d8 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -1325,16 +1325,16 @@ slots: and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. examples: - - value: CHEBI:5118 # fluoxetine - description: >- - In a MAXO annotation this would be a specialization in treatment of a disease. For example, - fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent - therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term - 'congenital myasthenic syndrome '4A.' - - value: GO:0005634 # nucleus - description: >- - In an expression annotation this would be a specialization in location of an anatomical entity. For example, - "expression in the nucleus of hepatic cells" would be a specialization of "expression in hepatic cells" + - value: CHEBI:5118 # fluoxetine + description: >- + In a MAXO annotation this would be a specialization in treatment of a disease. For example, + fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent + therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term + 'congenital myasthenic syndrome '4A.' + - value: GO:0005634 # nucleus + description: >- + In an expression annotation this would be a specialization in location of an anatomical entity. For example, + "expression in the nucleus of hepatic cells" would be a specialization of "expression in hepatic cells" aspect qualifier: is_a: qualifier diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql index 849ee0394..1e0420552 100644 --- a/project/graphql/biolink_model.graphql +++ b/project/graphql/biolink_model.graphql @@ -404,6 +404,9 @@ type BehaviorToBehavioralFeatureAssociation implements EntityToPhenotypicFeature qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -680,6 +683,9 @@ type CaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -733,6 +739,9 @@ type CausalGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -1873,6 +1882,9 @@ type CorrelatedGeneToDiseaseAssociation implements EntityToDiseaseAssociationMix qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -2256,6 +2268,9 @@ type DiseaseToPhenotypicFeatureAssociation implements FrequencyQuantifier, Entit qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String } type Drug implements ChemicalOrDrugOrTreatment, OntologyClass @@ -2445,6 +2460,9 @@ type DruggableGeneToDiseaseAssociation implements EntityToDiseaseAssociationMixi qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -2617,6 +2635,9 @@ type EntityToPhenotypicFeatureAssociationMixin implements FrequencyQuantifier object: PhenotypicFeature! sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -2902,6 +2923,9 @@ type ExposureEventToPhenotypicFeatureAssociation implements EntityToPhenotypicFe qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -3170,6 +3194,9 @@ type GeneAsAModelOfDiseaseAssociation implements ModelToDiseaseAssociationMixin, qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -3256,6 +3283,9 @@ type GeneHasVariantThatContributesToDiseaseAssociation qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -3379,6 +3409,9 @@ type GeneToDiseaseAssociation implements EntityToDiseaseAssociationMixin, GeneTo qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -3436,6 +3469,9 @@ type GeneToDiseaseOrPhenotypicFeatureAssociation implements EntityToPhenotypicFe qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -3846,6 +3882,9 @@ type GeneToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureAsso qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -4228,6 +4267,9 @@ type GenotypeToPhenotypicFeatureAssociation implements EntityToPhenotypicFeature qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double @@ -6022,6 +6064,9 @@ type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatur hasQuotient: Double hasPercentage: Double diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String } type PhenotypicQuality @@ -7501,6 +7546,9 @@ type VariantToPhenotypicFeatureAssociation implements VariantToEntityAssociation qualifiedPredicate: String sexQualifier: BiologicalSex diseaseContextQualifier: Disease + subjectSpecializationQualifier: Uriorcurie + objectSpecializationQualifier: Uriorcurie + anatomicalContextQualifier: String hasCount: Integer hasTotal: Integer hasQuotient: Double diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld index 62518fbb8..9e6525f07 100644 --- a/project/jsonld/biolink_model.context.jsonld +++ b/project/jsonld/biolink_model.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-11-07T15:54:30", + "generation_date": "2024-11-07T16:11:25", "source": "biolink_model.yaml" }, "@context": { @@ -1845,6 +1845,10 @@ "object_part_qualifier": { "@id": "object_part_qualifier" }, + "object_specialization_qualifier": { + "@type": "xsd:anyURI", + "@id": "object_specialization_qualifier" + }, "occurs_in": { "@type": "@id", "@id": "occurs_in" @@ -2261,6 +2265,7 @@ "@id": "subject_part_qualifier" }, "subject_specialization_qualifier": { + "@type": "xsd:anyURI", "@id": "subject_specialization_qualifier" }, "summary": { diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld index ac4b99bd9..0ab2aef29 100644 --- a/project/jsonld/biolink_model.jsonld +++ b/project/jsonld/biolink_model.jsonld @@ -3911,13 +3911,13 @@ "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", "examples": [ { - "value": "CHEBI:24431", + "value": "CHEBI:5118", "description": "In a MAXO annotation this would be a specialization in treatment of a disease. For example, fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term 'congenital myasthenic syndrome '4A.'", "@type": "Example" }, { - "value": "CL:0000123", - "description": "In an expression annotation this would be a specialization in location of an anatomical entity. For example, \"expression in the nucleas of hepatic cells\" would be a specialization of \"expression in hepatic cells\"", + "value": "GO:0005634", + "description": "In an expression annotation this would be a specialization in location of an anatomical entity. For example, \"expression in the nucleus of hepatic cells\" would be a specialization of \"expression in hepatic cells\"", "@type": "Example" } ], @@ -4165,9 +4165,18 @@ "name": "subject_specialization_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/subject_specialization_qualifier", "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "in_subset": [ + "translator_minimal" + ], "from_schema": "https://w3id.org/biolink/biolink-model", + "is_a": "specialization_qualifier", + "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_specialization_qualifier", - "range": "string", + "owner": "EntityToPhenotypicFeatureAssociationMixin", + "domain_of": [ + "EntityToPhenotypicFeatureAssociationMixin" + ], + "range": "uriorcurie", "@type": "SlotDefinition" }, { @@ -4347,6 +4356,24 @@ "range": "string", "@type": "SlotDefinition" }, + { + "name": "object_specialization_qualifier", + "definition_uri": "https://w3id.org/biolink/vocab/object_specialization_qualifier", + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "in_subset": [ + "translator_minimal" + ], + "from_schema": "https://w3id.org/biolink/biolink-model", + "is_a": "specialization_qualifier", + "domain": "Association", + "slot_uri": "https://w3id.org/biolink/vocab/object_specialization_qualifier", + "owner": "EntityToPhenotypicFeatureAssociationMixin", + "domain_of": [ + "EntityToPhenotypicFeatureAssociationMixin" + ], + "range": "uriorcurie", + "@type": "SlotDefinition" + }, { "name": "object_form_or_variant_qualifier", "definition_uri": "https://w3id.org/biolink/vocab/object_form_or_variant_qualifier", @@ -4564,12 +4591,13 @@ "is_a": "statement_qualifier", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/anatomical_context_qualifier", - "owner": "GeneAffectsChemicalAssociation", + "owner": "EntityToPhenotypicFeatureAssociationMixin", "domain_of": [ "PredicateMapping", "ChemicalGeneInteractionAssociation", "ChemicalAffectsGeneAssociation", - "GeneAffectsChemicalAssociation" + "GeneAffectsChemicalAssociation", + "EntityToPhenotypicFeatureAssociationMixin" ], "range": "string", "@type": "SlotDefinition" @@ -31023,7 +31051,7 @@ { "name": "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", "definition_uri": "https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", - "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.", + "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is a secondary undesirable effect.", "from_schema": "https://w3id.org/biolink/biolink-model", "is_a": "Association", "mixins": [ @@ -32140,6 +32168,9 @@ "entity_to_phenotypic_feature_association_mixin_object", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -32245,7 +32276,10 @@ "has_total", "has_quotient", "has_percentage", - "disease_context_qualifier" + "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier" ], "slot_usage": {}, "class_uri": "https://w3id.org/biolink/vocab/PhenotypicFeatureToPhenotypicFeatureAssociation", @@ -32556,6 +32590,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -32626,6 +32663,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -32705,7 +32745,10 @@ "object_direction_qualifier", "qualified_predicate", "sex_qualifier", - "disease_context_qualifier" + "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier" ], "slot_usage": {}, "class_uri": "https://w3id.org/biolink/vocab/DiseaseToPhenotypicFeatureAssociation", @@ -32773,6 +32816,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -32843,6 +32889,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -32964,6 +33013,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -33031,6 +33083,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -33110,6 +33165,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -33180,6 +33238,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -33250,6 +33311,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -33318,6 +33382,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -33705,6 +33772,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -33922,6 +33992,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -34358,6 +34431,9 @@ "qualified_predicate", "sex_qualifier", "disease_context_qualifier", + "subject_specialization_qualifier", + "object_specialization_qualifier", + "anatomical_context_qualifier", "has_count", "has_total", "has_quotient", @@ -35795,9 +35871,9 @@ ], "metamodel_version": "1.7.0", "source_file": "biolink_model.yaml", - "source_file_date": "2024-11-07T15:54:25", - "source_file_size": 402910, - "generation_date": "2024-11-07T15:54:33", + "source_file_date": "2024-11-07T16:11:20", + "source_file_size": 403672, + "generation_date": "2024-11-07T16:11:27", "@type": "SchemaDefinition", "@context": [ "project/jsonld/biolink_model.context.jsonld", diff --git a/project/jsonschema/biolink_model.schema.json b/project/jsonschema/biolink_model.schema.json index 71a567ed5..0a7eeee8b 100644 --- a/project/jsonschema/biolink_model.schema.json +++ b/project/jsonschema/biolink_model.schema.json @@ -2153,6 +2153,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -2346,6 +2353,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -2495,6 +2509,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -3938,6 +3959,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -4131,6 +4159,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -4280,6 +4315,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -4335,6 +4377,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -4528,6 +4577,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -4674,6 +4730,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -8110,7 +8173,7 @@ }, "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.", + "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is a secondary undesirable effect.", "properties": { "FDA_adverse_event_level": { "$ref": "#/$defs/FDAIDAAdverseEventEnum", @@ -12324,6 +12387,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -12517,6 +12587,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -12663,6 +12740,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -14889,6 +14973,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -15082,6 +15173,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "onset_qualifier": { "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject.", "type": [ @@ -15238,6 +15336,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -16301,6 +16406,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -16494,6 +16606,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -16640,6 +16759,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -18894,6 +19020,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -19087,6 +19220,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -19236,6 +19376,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -20617,6 +20764,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -20810,6 +20964,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -20956,6 +21117,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -21148,6 +21316,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -21341,6 +21516,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -21494,6 +21676,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -21966,6 +22155,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -22159,6 +22355,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -22305,6 +22508,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -22360,6 +22570,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -22553,6 +22770,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -22699,6 +22923,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -25036,6 +25267,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -25229,6 +25467,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -25375,6 +25620,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -27703,6 +27955,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -27896,6 +28155,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -28045,6 +28311,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -39156,6 +39429,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -39349,6 +39629,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -39498,6 +39785,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", @@ -49060,6 +49354,13 @@ "null" ] }, + "anatomical_context_qualifier": { + "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", + "type": [ + "string", + "null" + ] + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "enum": [ @@ -49253,6 +49554,13 @@ "null" ] }, + "object_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": [ @@ -49402,6 +49710,13 @@ "null" ] }, + "subject_specialization_qualifier": { + "description": "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.", + "type": [ + "string", + "null" + ] + }, "timepoint": { "description": "a point in time", "format": "time", diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl index a0cc7ecba..73605d032 100644 --- a/project/owl/biolink_model.owl.ttl +++ b/project/owl/biolink_model.owl.ttl @@ -123,10 +123,10 @@ biolink:HospitalizationOutcome a owl:Class ; biolink:MappingCollection a owl:Class ; rdfs:label "mapping collection" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:PredicateMapping ; owl:onProperty biolink:predicate_mappings ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PredicateMapping ; + owl:minCardinality 0 ; owl:onProperty biolink:predicate_mappings ], linkml:ClassDefinition ; skos:definition "A collection of deprecated mappings." ; @@ -1312,12 +1312,6 @@ biolink:severity_qualifier a owl:ObjectProperty ; skos:definition "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject" ; skos:inScheme . -biolink:specialization_qualifier a owl:DatatypeProperty ; - rdfs:label "specialization qualifier" ; - rdfs:subPropertyOf biolink:qualifier ; - skos:definition "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; - skos:inScheme . - biolink:start_coordinate a owl:DatatypeProperty ; rdfs:label "start coordinate" ; rdfs:subPropertyOf biolink:base_coordinate ; @@ -1334,11 +1328,6 @@ biolink:subject_location_in_text a owl:DatatypeProperty ; skos:definition "Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion." ; skos:inScheme . -biolink:subject_specialization_qualifier a owl:DatatypeProperty ; - rdfs:label "subject specialization qualifier" ; - skos:definition "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; - skos:inScheme . - biolink:superclass_of a owl:ObjectProperty ; rdfs:label "superclass of" ; rdfs:domain biolink:OntologyClass ; @@ -2665,14 +2654,17 @@ biolink:AccessibleDnaRegion a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], @@ -2680,16 +2672,13 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; @@ -2698,32 +2687,32 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; skos:inScheme . @@ -2821,19 +2810,19 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:BehavioralFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; skos:inScheme . @@ -2861,20 +2850,20 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:type ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; skos:inScheme . @@ -2889,10 +2878,10 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; skos:inScheme . @@ -2900,29 +2889,29 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:label "causal gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3015,20 +3004,20 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:CellLine ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; skos:inScheme . @@ -3042,166 +3031,166 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme . @@ -3209,73 +3198,73 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A regulatory relationship between two genes" ; skos:inScheme . @@ -3284,31 +3273,28 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_part_qualifier ], @@ -3316,74 +3302,77 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], biolink:Association ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; skos:exactMatch SIO:001257 ; @@ -3395,17 +3384,17 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; skos:inScheme . @@ -3433,37 +3422,37 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:catalyst_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:catalyst_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], biolink:ChemicalToChemicalAssociation ; skos:definition "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; @@ -3474,18 +3463,18 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; skos:inScheme ; @@ -3494,22 +3483,22 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalToPathwayAssociation a owl:Class ; rdfs:label "chemical to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -3563,10 +3552,10 @@ biolink:ClinicalMeasurement a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute_type ], biolink:ClinicalAttribute ; skos:definition "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; @@ -3629,11 +3618,14 @@ biolink:ConfidenceLevel a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationContentEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:qualifiers ], @@ -3642,25 +3634,22 @@ biolink:ContributorAssociation a owl:Class ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:InformationContentEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; skos:inScheme . @@ -3668,29 +3657,29 @@ biolink:ContributorAssociation a owl:Class ; biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; rdfs:label "correlated gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3708,10 +3697,10 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; rdfs:label "disease or phenotypic feature exposure" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin ], + owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:PathologicalEntityMixin ], biolink:Attribute ; skos:definition "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; skos:inScheme . @@ -3719,15 +3708,6 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:allValuesFrom biolink:GeneticInheritance ; owl:onProperty biolink:object ], [ a owl:Restriction ; @@ -3739,6 +3719,15 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; skos:inScheme . @@ -3749,13 +3738,13 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; @@ -3776,29 +3765,20 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:onset_qualifier ], @@ -3808,9 +3788,18 @@ biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:PhenotypicFeature ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:Association ; skos:closeMatch dcid:DiseaseSymptomAssociation ; skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; @@ -3862,6 +3851,9 @@ biolink:DrugToEntityAssociationMixin a owl:Class ; biolink:DrugToGeneAssociation a owl:Class ; rdfs:label "drug to gene association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], [ a owl:Restriction ; @@ -3870,9 +3862,6 @@ biolink:DrugToGeneAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a drug and a gene or gene product." ; skos:inScheme ; @@ -3910,20 +3899,17 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_evidence ], + [ a owl:Restriction ; owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -3933,12 +3919,15 @@ biolink:DruggableGeneToDiseaseAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3946,22 +3935,22 @@ biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_approval_status ], + owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ResearchPhaseEnum ; + owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ResearchPhaseEnum ; - owl:onProperty biolink:max_research_phase ], + owl:minCardinality 0 ; + owl:onProperty biolink:clinical_approval_status ], biolink:Association ; skos:inScheme . @@ -3980,20 +3969,20 @@ biolink:EntityToOutcomeAssociationMixin a owl:Class ; biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "entity to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ResearchPhaseEnum ; - owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ResearchPhaseEnum ; + owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:clinical_approval_status ], @@ -4037,12 +4026,6 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; @@ -4054,6 +4037,12 @@ biolink:ExonToTranscriptRelationship a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:Exon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" ; skos:inScheme . @@ -4061,26 +4050,26 @@ biolink:ExonToTranscriptRelationship a owl:Class ; biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:population_context_qualifier ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:temporal_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:temporal_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], biolink:Association ; skos:definition "An association between an exposure event and an outcome." ; skos:inScheme . @@ -4088,16 +4077,16 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ExposureEvent ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; @@ -4156,175 +4145,175 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; rdfs:label "gene affects chemical association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_derivative_qualifier ], biolink:Association ; skos:definition "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; skos:inScheme . @@ -4335,8 +4324,8 @@ biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -4344,49 +4333,49 @@ biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -4673,68 +4662,68 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; biolink:GeneRegulatesGeneAssociation a owl:Class ; rdfs:label "gene regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . @@ -4743,50 +4732,50 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" ; @@ -4795,16 +4784,16 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneExpressionMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; @@ -4813,32 +4802,32 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneFamily ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneFamily ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; skos:inScheme . @@ -4846,29 +4835,29 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -4879,32 +4868,32 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneProductMixin ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneProductMixin ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; skos:inScheme . @@ -4912,20 +4901,20 @@ biolink:GeneToGeneProductRelationship a owl:Class ; biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -4937,19 +4926,16 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -4957,6 +4943,9 @@ biolink:GeneToPathwayAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; skos:inScheme . @@ -4964,17 +4953,11 @@ biolink:GeneToPathwayAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], @@ -4983,6 +4966,12 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -4994,14 +4983,14 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; biolink:Genome a owl:Class ; rdfs:label "genome" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:closeMatch dcid:GenomeAssemblyUnit ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; @@ -5026,10 +5015,10 @@ biolink:GenomicBackgroundExposure a owl:Class ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:OntologyClass ], biolink:Attribute ; skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; skos:inScheme . @@ -5037,52 +5026,52 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], biolink:GenotypeToDiseaseAssociation ; skos:inScheme . biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; skos:inScheme . @@ -5093,29 +5082,29 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ; skos:inScheme . @@ -5123,29 +5112,29 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; skos:inScheme . @@ -5153,14 +5142,14 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -5168,16 +5157,16 @@ biolink:GenotypeToVariantAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." ; @@ -5217,14 +5206,14 @@ biolink:GeographicExposure a owl:Class ; biolink:GeographicLocationAtTime a owl:Class ; rdfs:label "geographic location at time" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; owl:allValuesFrom xsd:time ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ], biolink:GeographicLocation ; skos:definition "a location that can be described in lat/long coordinates, for a particular time" ; skos:inScheme . @@ -5245,10 +5234,10 @@ biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], @@ -5282,20 +5271,20 @@ biolink:Human a owl:Class ; biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], @@ -5303,11 +5292,11 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; skos:inScheme . @@ -5386,17 +5375,17 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:label "macromolecular machine to biological process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; skos:inScheme . @@ -5404,10 +5393,10 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; rdfs:label "macromolecular machine to cellular component association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:CellularComponent ; @@ -5422,16 +5411,16 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; rdfs:label "macromolecular machine to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; @@ -5441,31 +5430,31 @@ biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MaterialSample ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." ; skos:inScheme . @@ -5499,23 +5488,23 @@ biolink:MicroRNA a owl:Class ; biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; skos:inScheme . @@ -5526,20 +5515,20 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:MolecularActivity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; skos:inScheme . @@ -5549,30 +5538,30 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; skos:inScheme . @@ -5580,32 +5569,38 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:population_context_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], @@ -5614,43 +5609,37 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:population_context_qualifier ], biolink:Association ; skos:inScheme . @@ -5665,13 +5654,13 @@ biolink:NucleosomeModification a owl:Class ; rdfs:label "nucleosome modification" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:EpigenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity ], + owl:someValuesFrom biolink:GeneProductIsoformMixin ], biolink:BiologicalEntity ; skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; skos:inScheme . @@ -5685,32 +5674,32 @@ biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -5720,41 +5709,41 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:associated_environmental_context ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:associated_environmental_context ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; skos:inScheme . @@ -5762,32 +5751,32 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; skos:inScheme . @@ -5795,22 +5784,22 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:IndividualOrganism ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:IndividualOrganism ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -5818,20 +5807,20 @@ biolink:OrganismToOrganismAssociation a owl:Class ; biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismalEntity ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:allValuesFrom biolink:OrganismalEntity ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -5839,49 +5828,49 @@ biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 0 ; owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:interacting_molecules_category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:interacting_molecules_category ], + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; skos:inScheme . @@ -5973,11 +5962,8 @@ biolink:Phenomenon a owl:Class ; biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; rdfs:label "phenotypic feature to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], @@ -5985,8 +5971,11 @@ biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . @@ -6044,32 +6033,32 @@ biolink:Plant a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a two populations" ; skos:inScheme . @@ -6086,194 +6075,194 @@ biolink:PosttranslationalModification a owl:Class ; biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:mapped_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:broad_match ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:narrow_match ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:mapped_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:broad_match ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:mapped_predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:exact_match ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:broad_match ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:causal_mechanism_qualifier ], linkml:ClassDefinition ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; skos:inScheme . @@ -6289,6 +6278,12 @@ biolink:PreprintPublication a owl:Class ; biolink:ProcessRegulatesProcessAssociation a owl:Class ; rdfs:label "process regulates process association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; @@ -6300,23 +6295,17 @@ biolink:ProcessRegulatesProcessAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - biolink:Association ; - skos:definition "Describes a regulatory relationship between two genes or gene products." ; + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + biolink:Association ; + skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . biolink:ProcessedMaterial a owl:Class ; @@ -6409,13 +6398,13 @@ biolink:RNAProductIsoform a owl:Class ; biolink:ReactionToCatalystAssociation a owl:Class ; rdfs:label "reaction to catalyst association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:ReactionToParticipantAssociation ; skos:inScheme . @@ -6427,10 +6416,10 @@ biolink:ReagentTargetedGene a owl:Class ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:altLabel "sequence targeting reagent" ; skos:definition "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; @@ -6507,23 +6496,23 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Treatment ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Treatment ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:inScheme ; @@ -6532,47 +6521,47 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:issue ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:issue ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:issue ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], biolink:Publication ; skos:altLabel "journal" ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; @@ -6621,10 +6610,10 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:SocioeconomicAttribute ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -6670,23 +6659,23 @@ biolink:StudyVariable a owl:Class ; biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -6708,18 +6697,18 @@ biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -6730,17 +6719,17 @@ biolink:TranscriptToGeneRelationship a owl:Class ; biolink:TranscriptionFactorBindingSite a owl:Class ; rdfs:label "transcription factor binding site" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], biolink:RegulatoryRegion ; skos:altLabel "binding site", "tf binding site" ; @@ -6751,37 +6740,37 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "variant as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:VariantToDiseaseAssociation ; skos:inScheme . biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" ; skos:inScheme . @@ -6792,76 +6781,76 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], biolink:Association ; skos:inScheme . biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_count ], + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQualifierMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_count ], biolink:Association ; skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ; skos:inScheme . @@ -7333,6 +7322,12 @@ biolink:similar_to a owl:DatatypeProperty, skos:inScheme ; biolink:canonical_predicate true . +biolink:specialization_qualifier a owl:DatatypeProperty ; + rdfs:label "specialization qualifier" ; + rdfs:subPropertyOf biolink:qualifier ; + skos:definition "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + skos:inScheme . + biolink:subject_category_closure a owl:ObjectProperty ; rdfs:label "subject category closure" ; rdfs:domain biolink:Association ; @@ -7420,9 +7415,6 @@ biolink:AdministrativeEntity a owl:Class ; biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; @@ -7430,31 +7422,34 @@ biolink:Article a owl:Class ; owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:issue ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:published_in ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; skos:exactMatch fabio:article, @@ -7487,29 +7482,29 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:chapter ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:chapter ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:published_in ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:chapter ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:volume ], @@ -7530,13 +7525,13 @@ biolink:Case a owl:Class ; biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "cell line to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -7563,14 +7558,14 @@ biolink:ChemicalEntityToEntityAssociationMixin a owl:Class ; biolink:ChemicalExposure a owl:Class ; rdfs:label "chemical exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], biolink:Attribute ; skos:definition "A chemical exposure is an intake of a particular chemical entity." ; skos:exactMatch ECTO:9000000, @@ -7580,31 +7575,31 @@ biolink:ChemicalExposure a owl:Class ; biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; - owl:onProperty biolink:FDA_adverse_event_level ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], biolink:Association ; - skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; + skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is a secondary undesirable effect." ; skos:inScheme . a owl:Class ; @@ -7737,38 +7732,17 @@ biolink:GeneFamily a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:start_interbase_coordinate ], - [ a owl:Restriction ; owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:strand ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhaseEnum ; - owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:strand ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:genome_build ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; - owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], @@ -7777,37 +7751,58 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:PhaseEnum ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:start_interbase_coordinate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:phase ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:StrandEnum ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:phase ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:genome_build ], + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phase ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:object ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -7817,38 +7812,38 @@ biolink:GenomicSequenceLocalization a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7862,22 +7857,22 @@ biolink:GeographicLocation a owl:Class ; rdfs:label "geographic location" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:latitude ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; + owl:maxCardinality 1 ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:latitude ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:latitude ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:latitude ], + owl:onProperty biolink:longitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, @@ -7919,14 +7914,14 @@ biolink:OrganismTaxonToEntityAssociation a owl:Class ; biolink:PairwiseGeneToGeneInteraction a owl:Class ; rdfs:label "pairwise gene to gene interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; skos:inScheme ; @@ -7944,10 +7939,10 @@ biolink:Polypeptide a owl:Class ; rdfs:label "polypeptide" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:BiologicalEntity ; skos:altLabel "amino acid entity" ; skos:definition "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; @@ -7959,41 +7954,41 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stoichiometry ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_direction ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:allValuesFrom xsd:integer ; owl:onProperty biolink:stoichiometry ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:allValuesFrom biolink:ReactionDirectionEnum ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stoichiometry ], + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ReactionSideEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_side ], + owl:minCardinality 0 ; + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ReactionSideEnum ; + owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:reaction_side ], biolink:ChemicalToChemicalAssociation ; skos:inScheme . @@ -8026,28 +8021,28 @@ biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_device ], + owl:onProperty biolink:has_drug ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Procedure ; + owl:minCardinality 0 ; owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:allValuesFrom biolink:Device ; owl:onProperty biolink:has_device ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_device ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Procedure ; + owl:onProperty biolink:has_procedure ], biolink:NamedThing ; skos:altLabel "medical action", "medical intervention" ; @@ -8060,38 +8055,38 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -8099,25 +8094,25 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; @@ -8539,6 +8534,13 @@ biolink:object_namespace a owl:DatatypeProperty ; skos:inScheme ; biolink:denormalized true . +biolink:object_specialization_qualifier a owl:DatatypeProperty ; + rdfs:label "object specialization qualifier" ; + rdfs:range xsd:anyURI ; + rdfs:subPropertyOf biolink:specialization_qualifier ; + skos:definition "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + skos:inScheme . + biolink:onset_qualifier a owl:ObjectProperty ; rdfs:label "onset qualifier" ; rdfs:range biolink:Onset ; @@ -8706,6 +8708,13 @@ biolink:subject_namespace a owl:DatatypeProperty ; skos:inScheme ; biolink:denormalized true . +biolink:subject_specialization_qualifier a owl:DatatypeProperty ; + rdfs:label "subject specialization qualifier" ; + rdfs:range xsd:anyURI ; + rdfs:subPropertyOf biolink:specialization_qualifier ; + skos:definition "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + skos:inScheme . + biolink:summary a owl:DatatypeProperty ; rdfs:label "summary" ; rdfs:domain biolink:Publication ; @@ -8790,19 +8799,19 @@ biolink:ActivityAndBehavior a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -8841,31 +8850,31 @@ biolink:ChemicalToChemicalAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; @@ -8943,17 +8952,8 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], @@ -8961,37 +8961,46 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:inScheme ; @@ -9048,23 +9057,23 @@ biolink:Onset a owl:Class ; biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], @@ -9114,9 +9123,6 @@ biolink:ReactionSideEnum a owl:Class ; biolink:RegulatoryRegion a owl:Class ; rdfs:label "regulatory region" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; @@ -9125,6 +9131,9 @@ biolink:RegulatoryRegion a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:altLabel "regulatory element" ; skos:definition "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; @@ -9475,13 +9484,13 @@ biolink:CellularComponent a owl:Class ; biolink:DatasetDistribution a owl:Class ; rdfs:label "dataset distribution" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:distribution_download_url ], biolink:InformationContentEntity ; skos:definition "an item that holds distribution level information about a dataset." ; @@ -9492,18 +9501,18 @@ biolink:DatasetSummary a owl:Class ; rdfs:label "dataset summary" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:source_logo ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:source_logo ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:source_logo ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:source_logo ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; @@ -9534,17 +9543,17 @@ biolink:GeneProductIsoformMixin a owl:Class ; biolink:GeneToGeneAssociation a owl:Class ; rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -9632,23 +9641,23 @@ biolink:Protein a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:has_unit ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_unit ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_numeric_value ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:has_unit ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; skos:inScheme . @@ -9663,13 +9672,13 @@ biolink:ResourceRoleEnum a owl:Class ; biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -9678,7 +9687,7 @@ biolink:SequenceFeatureRelationship a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; @@ -9800,31 +9809,31 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Dataset ; - owl:onProperty biolink:has_dataset ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_dataset ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DatasetDistribution ; owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:ingest_date ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Dataset ; + owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_distribution ], + owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:DatasetDistribution ; owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:ingest_date ], + owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:ingest_date ], biolink:InformationContentEntity ; skos:definition "an item that holds version level information about a dataset." ; @@ -9858,16 +9867,16 @@ biolink:FunctionalAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -10269,38 +10278,38 @@ biolink:CellularOrganism a owl:Class ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; - owl:onProperty biolink:highest_FDA_approval_status ], + owl:minCardinality 0 ; + owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; owl:allValuesFrom biolink:ApprovalStatusEnum ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:highest_FDA_approval_status ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], + owl:allValuesFrom biolink:ApprovalStatusEnum ; + owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:is_supplement ], + owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:routes_of_delivery ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; + owl:onProperty biolink:routes_of_delivery ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -10327,25 +10336,25 @@ biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], @@ -10364,20 +10373,26 @@ biolink:MacromolecularMachineMixin a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_output ], + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:maxCardinality 1 ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], + owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], @@ -10386,16 +10401,10 @@ biolink:MolecularActivity a owl:Class ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_output ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_input ], biolink:BiologicalProcessOrActivity ; skos:altLabel "molecular event", "molecular function", @@ -10415,37 +10424,37 @@ biolink:PhysicalEssenceOrOccurrent a owl:Class ; biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:resource_id ], - [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:resource_id ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:resource_id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:resource_role ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ResourceRoleEnum ; + owl:minCardinality 1 ; owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:resource_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:resource_role ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ResourceRoleEnum ; owl:onProperty biolink:resource_role ], biolink:InformationContentEntity ; skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; @@ -10779,10 +10788,10 @@ biolink:Drug a owl:Class ; rdfs:label "drug" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], biolink:MolecularMixture ; skos:broadMatch STY:T121 ; skos:definition "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; @@ -10798,21 +10807,21 @@ biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Zygosity ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_zygosity ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:Zygosity ; owl:onProperty biolink:has_zygosity ], biolink:BiologicalEntity ; skos:definition "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; @@ -10907,20 +10916,38 @@ biolink:AgentTypeEnum a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:description ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:deprecated ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:deprecated ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:description ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:type ], @@ -10929,46 +10956,28 @@ biolink:Entity a owl:Class ; owl:onProperty biolink:category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:description ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; - owl:onProperty biolink:has_attribute ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:deprecated ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:description ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_attribute ], + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], linkml:ClassDefinition ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; skos:inScheme . @@ -11048,6 +11057,9 @@ biolink:xref a owl:DatatypeProperty ; biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ThingWithTaxon ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; @@ -11056,9 +11068,6 @@ biolink:NucleicAcidEntity a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], biolink:MolecularEntity ; skos:altLabel "genomic entity", "sequence feature" ; @@ -11071,14 +11080,14 @@ biolink:NucleicAcidEntity a owl:Class ; biolink:OrganismalEntity a owl:Class ; rdfs:label "organismal entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_attribute ], + [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:SubjectOfInvestigation ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_attribute ], biolink:BiologicalEntity ; skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; skos:exactMatch , @@ -11093,13 +11102,6 @@ biolink:SubjectOfInvestigation a owl:Class ; skos:definition "An entity that has the role of being studied in an investigation, study, or experiment" ; skos:inScheme . -biolink:anatomical_context_qualifier a owl:DatatypeProperty ; - rdfs:label "anatomical context qualifier" ; - rdfs:subPropertyOf biolink:statement_qualifier ; - skos:definition "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - skos:editorialNote "Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ; - skos:inScheme . - biolink:object_form_or_variant_qualifier a owl:DatatypeProperty ; rdfs:label "object form or variant qualifier" ; rdfs:subPropertyOf biolink:form_or_variant_qualifier ; @@ -11163,38 +11165,38 @@ biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:PhysicalEntity ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], + owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhysicalEntity ; + owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], + owl:onProperty biolink:enabled_by ], biolink:BiologicalEntity ; skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; skos:inScheme . @@ -11203,37 +11205,37 @@ biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:address ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:address ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:affiliation ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:address ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:affiliation ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -11276,6 +11278,13 @@ biolink:PhysicalEssence a owl:Class ; skos:definition "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; skos:inScheme . +biolink:anatomical_context_qualifier a owl:DatatypeProperty ; + rdfs:label "anatomical context qualifier" ; + rdfs:subPropertyOf biolink:statement_qualifier ; + skos:definition "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + skos:editorialNote "Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs." ; + skos:inScheme . + biolink:name a owl:DatatypeProperty ; rdfs:label "name" ; rdfs:domain biolink:Entity ; @@ -11372,13 +11381,13 @@ biolink:DirectionQualifierEnum a owl:Class ; biolink:MolecularEntity a owl:Class ; rdfs:label "molecular entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:is_metabolite ], biolink:ChemicalEntity ; skos:definition "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; @@ -11428,41 +11437,41 @@ biolink:BiologicalProcess a owl:Class ; biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:creation_date ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:format ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:creation_date ], + owl:maxCardinality 1 ; + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:format ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:format ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:license ], + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:license ], + owl:maxCardinality 1 ; + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:allValuesFrom xsd:date ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:rights ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:rights ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:format ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:creation_date ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -11520,49 +11529,49 @@ biolink:CausalMechanismQualifierEnum a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_quantitative_value ], + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:has_attribute_type ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], biolink:NamedThing ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; @@ -11589,34 +11598,34 @@ biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:symbol ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:symbol ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct ], + owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:broadMatch ; skos:definition "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; @@ -11630,38 +11639,38 @@ biolink:Gene a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], biolink:BiologicalEntity ; skos:altLabel "allele" ; skos:closeMatch , @@ -11705,26 +11714,32 @@ biolink:AnatomicalEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:publication_type ], + [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:summary ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; + owl:minCardinality 0 ; owl:onProperty biolink:authors ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:pages ], + owl:minCardinality 0 ; + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:authors ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:keywords ], @@ -11732,41 +11747,35 @@ biolink:Publication a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:publication_type ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:summary ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:mesh_terms ], + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:authors ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:publication_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:pages ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:summary ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:pages ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:keywords ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:pages ], biolink:InformationContentEntity ; skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; skos:exactMatch IAO:0000311 ; @@ -11790,56 +11799,56 @@ biolink:BiologicalEntity a owl:Class ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:is_toxic ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:max_tolerated_dose ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:max_tolerated_dose ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:available_from ], + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:trade_name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; - owl:onProperty biolink:available_from ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:is_toxic ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:max_tolerated_dose ], + owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalRole ; owl:onProperty biolink:has_chemical_role ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_chemical_role ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:is_toxic ], biolink:NamedThing ; skos:broadMatch STY:T167 ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -11978,38 +11987,32 @@ biolink:association_slot a owl:DatatypeProperty ; biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_closure ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:KnowledgeLevelEnum ; - owl:onProperty biolink:knowledge_level ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:adjusted_p_value ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_category ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_label_closure ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -12017,68 +12020,77 @@ biolink:Association a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:knowledge_source ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:retrieval_source_ids ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:KnowledgeLevelEnum ; + owl:onProperty biolink:knowledge_level ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:agent_type ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category_closure ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:negated ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_label_closure ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:original_predicate ], + owl:allValuesFrom biolink:AgentTypeEnum ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:p_value ], + owl:onProperty biolink:subject_label_closure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:negated ], + owl:onProperty biolink:knowledge_level ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:subject_category ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Study ; + owl:onProperty biolink:has_supporting_studies ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:original_object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_namespace ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:allValuesFrom biolink:RetrievalSource ; owl:onProperty biolink:retrieval_source_ids ], @@ -12087,151 +12099,148 @@ biolink:Association a owl:Class ; owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_label_closure ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AgentTypeEnum ; - owl:onProperty biolink:agent_type ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_supporting_studies ], + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_closure ], + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_namespace ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:original_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_label_closure ], + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:p_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_source ], + owl:minCardinality 0 ; + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category_closure ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Study ; - owl:onProperty biolink:has_supporting_studies ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_namespace ], + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_closure ], + owl:minCardinality 1 ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:p_value ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_namespace ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_closure ], + owl:minCardinality 0 ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_object ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_category_closure ], + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:p_value ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_label_closure ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:negated ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -12251,38 +12260,38 @@ biolink:related_to_at_instance_level a owl:DatatypeProperty, biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:full_name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:full_name ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:provided_by ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:provided_by ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:provided_by ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; skos:exactMatch STY:T071, @@ -12335,436 +12344,423 @@ biolink:subject a owl:ObjectProperty ; skos:inScheme . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocation ; + rdfs:subClassOf biolink:ChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocation . + owl:someValuesFrom biolink:ChemicalExposure . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent . + rdfs:subClassOf biolink:Genome ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Genome . [] a owl:Restriction ; - rdfs:subClassOf biolink:Serial ; + rdfs:subClassOf biolink:NamedThing ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Serial . + owl:someValuesFrom biolink:NamedThing . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalEntity ; + rdfs:subClassOf biolink:ClinicalMeasurement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalEntity . + owl:someValuesFrom biolink:ClinicalMeasurement . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyPopulation ; + rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyPopulation . + owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThing ; + rdfs:subClassOf biolink:Event ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThing . + owl:someValuesFrom biolink:Event . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; + rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . + owl:someValuesFrom biolink:NucleicAcidSequenceMotif . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SpecificityQuantifier . + rdfs:subClassOf biolink:LifeStage ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:LifeStage . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidSequenceMotif . + owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetSummary ; + rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetSummary . + owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseAssociation . + owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiagnosticAid ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiagnosticAid . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phenotypic_state ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:expression_site ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin . + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntity ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntity . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexMolecularMixture ; + rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexMolecularMixture . + owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicAttribute ; + rdfs:subClassOf biolink:Fungus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicAttribute . + owl:someValuesFrom biolink:Fungus . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularMixture ; + rdfs:subClassOf biolink:OrganismTaxon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularMixture . + owl:someValuesFrom biolink:OrganismTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularComponent ; + rdfs:subClassOf biolink:Patent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularComponent . + owl:someValuesFrom biolink:Patent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genotype ; + rdfs:subClassOf biolink:Agent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genotype . + owl:someValuesFrom biolink:Agent . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicExposure ; + rdfs:subClassOf biolink:PhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicExposure . + owl:someValuesFrom biolink:PhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + rdfs:subClassOf biolink:SequenceVariant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneProductRelationship . + owl:someValuesFrom biolink:SequenceVariant . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BioticExposure ; + rdfs:subClassOf biolink:Treatment ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BioticExposure . + owl:someValuesFrom biolink:Treatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Outcome ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLine ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLine . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ActivityAndBehavior . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; + rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . + owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Plant ; + rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Plant . + owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + rdfs:subClassOf biolink:PlanetaryEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . + owl:someValuesFrom biolink:PlanetaryEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxon ; + rdfs:subClassOf biolink:WebPage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxon . + owl:someValuesFrom biolink:WebPage . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin . + rdfs:subClassOf biolink:Attribute ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Attribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; + rdfs:subClassOf biolink:Publication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalStructure . + owl:someValuesFrom biolink:Publication . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiagnosticAid ; + rdfs:subClassOf biolink:RNAProductIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiagnosticAid . + owl:someValuesFrom biolink:RNAProductIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; + rdfs:subClassOf biolink:VariantToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneAssociation . + owl:someValuesFrom biolink:VariantToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ConfidenceLevel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ConfidenceLevel . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToCatalystAssociation . + owl:someValuesFrom biolink:ChemicalToPathwayAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Food ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Food . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Vertebrate ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Vertebrate . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeature ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeature . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Onset ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Onset . + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Procedure ; + rdfs:subClassOf biolink:ComplexChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Procedure . + owl:someValuesFrom biolink:ComplexChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:SocioeconomicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:SocioeconomicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; + rdfs:subClassOf biolink:MaterialSample ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalExposure . + owl:someValuesFrom biolink:MaterialSample . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + rdfs:subClassOf biolink:IndividualOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + owl:someValuesFrom biolink:IndividualOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . - -[] a owl:Restriction ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidEntity . + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetVersion ; + rdfs:subClassOf biolink:TranscriptToGeneRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetVersion . + owl:someValuesFrom biolink:TranscriptToGeneRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:Haplotype ; + rdfs:subClassOf biolink:Entity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Haplotype . + owl:someValuesFrom biolink:Entity . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetDistribution ; + rdfs:subClassOf biolink:LogOddsAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetDistribution . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent . + owl:someValuesFrom biolink:LogOddsAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BookChapter ; + rdfs:subClassOf biolink:PhysiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BookChapter . + owl:someValuesFrom biolink:PhysiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalRole ; + rdfs:subClassOf biolink:OrganismToOrganismAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalRole . + owl:someValuesFrom biolink:OrganismToOrganismAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin . + owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . + owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:TaxonToTaxonAssociation ; + rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TaxonToTaxonAssociation . + owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Protein ; + rdfs:subClassOf biolink:NucleosomeModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Protein . + owl:someValuesFrom biolink:NucleosomeModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; + rdfs:subClassOf biolink:Behavior ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . + owl:someValuesFrom biolink:Behavior . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPopulationAssociation ; + rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPopulationAssociation . + owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Human ; + rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Human . + owl:someValuesFrom biolink:DrugToGeneInteractionExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; + rdfs:subClassOf biolink:AdministrativeEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . + owl:someValuesFrom biolink:AdministrativeEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; @@ -12772,217 +12768,129 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct . + rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalExposure ; + rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalExposure . + owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProduct ; + rdfs:subClassOf biolink:DatasetSummary ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProduct . + owl:someValuesFrom biolink:DatasetSummary . [] a owl:Restriction ; - rdfs:subClassOf biolink:IndividualOrganism ; + rdfs:subClassOf biolink:EnvironmentalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IndividualOrganism . + owl:someValuesFrom biolink:EnvironmentalProcess . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . + rdfs:subClassOf biolink:Study ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Study . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; + rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . + owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; + rdfs:subClassOf biolink:FunctionalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . + owl:someValuesFrom biolink:FunctionalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalCourse ; + rdfs:subClassOf biolink:BioticExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalCourse . + owl:someValuesFrom biolink:BioticExposure . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . + rdfs:subClassOf biolink:Food ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Food . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReagentTargetedGene ; + rdfs:subClassOf biolink:BiologicalSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReagentTargetedGene . + owl:someValuesFrom biolink:BiologicalSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:Transcript ; + rdfs:subClassOf biolink:DatasetVersion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Transcript . + owl:someValuesFrom biolink:DatasetVersion . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene_or_gene_product ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin . + owl:someValuesFrom biolink:SpecificityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:SiRNA ; + rdfs:subClassOf biolink:BiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SiRNA . + owl:someValuesFrom biolink:BiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CommonDataElement ; + rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CommonDataElement . + owl:someValuesFrom biolink:EnvironmentalFoodContaminant . [] a owl:Restriction ; - rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . + owl:someValuesFrom biolink:VariantToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntity ; + rdfs:subClassOf biolink:CellularOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntity . + owl:someValuesFrom biolink:CellularOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; + rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:ProteinDomain ; @@ -12990,704 +12898,681 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:ProteinDomain . [] a owl:Restriction ; - rdfs:subClassOf biolink:LifeStage ; + rdfs:subClassOf biolink:ChemicalMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LifeStage . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SensitivityQuantifier . + owl:someValuesFrom biolink:ChemicalMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:Bacterium ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . + owl:someValuesFrom biolink:Bacterium . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Outcome . + rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . + owl:someValuesFrom biolink:Occurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Zygosity ; + rdfs:subClassOf biolink:GeographicLocation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Zygosity . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:GeographicLocation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PosttranslationalModification ; + rdfs:subClassOf biolink:SiRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PosttranslationalModification . + owl:someValuesFrom biolink:SiRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariant ; + rdfs:subClassOf biolink:BehavioralFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariant . + owl:someValuesFrom biolink:BehavioralFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cohort ; + rdfs:subClassOf biolink:ContributorAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cohort . + owl:someValuesFrom biolink:ContributorAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicSex ; + rdfs:subClassOf biolink:MolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicSex . + owl:someValuesFrom biolink:MolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:Treatment ; + rdfs:subClassOf biolink:GenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Treatment . + owl:someValuesFrom biolink:GenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConfidenceLevel ; + rdfs:subClassOf biolink:TextMiningResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConfidenceLevel . + owl:someValuesFrom biolink:TextMiningResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamily ; + rdfs:subClassOf biolink:FoodAdditive ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamily . + owl:someValuesFrom biolink:FoodAdditive . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; + rdfs:subClassOf biolink:GenomicBackgroundExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalAssociation . + owl:someValuesFrom biolink:GenomicBackgroundExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; + rdfs:subClassOf biolink:ClinicalTrial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + owl:someValuesFrom biolink:ClinicalTrial . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; + rdfs:subClassOf biolink:GrossAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . + owl:someValuesFrom biolink:GrossAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSample ; + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSample . + owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CodingSequence ; + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CodingSequence . + owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinFamily ; + rdfs:subClassOf biolink:ComplexMolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinFamily . + owl:someValuesFrom biolink:ComplexMolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + rdfs:subClassOf biolink:Zygosity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseMolecularInteraction . + owl:someValuesFrom biolink:Zygosity . [] a owl:Restriction ; - rdfs:subClassOf biolink:WebPage ; + rdfs:subClassOf biolink:OrganismalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:WebPage . + owl:someValuesFrom biolink:OrganismalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Publication ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Publication . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Case ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ContributorAssociation ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ContributorAssociation . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PlanetaryEntity ; + rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PlanetaryEntity . + owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularOrganism ; + rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularOrganism . + owl:someValuesFrom biolink:TranscriptionFactorBindingSite . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:ConceptCountAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:ConceptCountAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:Gene ; + rdfs:subClassOf biolink:PhenotypicQuality ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Gene . + owl:someValuesFrom biolink:PhenotypicQuality . [] a owl:Restriction ; - rdfs:subClassOf biolink:Snv ; + rdfs:subClassOf biolink:ProteinIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Snv . + owl:someValuesFrom biolink:ProteinIsoform . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CellLine ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MicroRNA ; + rdfs:subClassOf biolink:GenotypeToVariantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MicroRNA . + owl:someValuesFrom biolink:GenotypeToVariantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcess ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcess . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathologicalEntityMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . + owl:someValuesFrom biolink:GeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:FoodAdditive ; + rdfs:subClassOf biolink:DrugExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FoodAdditive . + owl:someValuesFrom biolink:DrugExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleosomeModification ; + rdfs:subClassOf biolink:NucleicAcidEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleosomeModification . + owl:someValuesFrom biolink:NucleicAcidEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Fungus ; + rdfs:subClassOf biolink:Drug ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Fungus . + owl:someValuesFrom biolink:Drug . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyResult ; + rdfs:subClassOf biolink:Pathway ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyResult . + owl:someValuesFrom biolink:Pathway . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; + rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence . + rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PairwiseMolecularInteraction . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . + owl:someValuesFrom biolink:DrugToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessedMaterial ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessedMaterial . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:RelationshipQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:CodingSequence ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:CodingSequence . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyVariable ; + rdfs:subClassOf biolink:Invertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyVariable . + owl:someValuesFrom biolink:Invertebrate . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin . + owl:someValuesFrom biolink:Outcome . [] a owl:Restriction ; - rdfs:subClassOf biolink:SmallMolecule ; + rdfs:subClassOf biolink:PreprintPublication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SmallMolecule . + owl:someValuesFrom biolink:PreprintPublication . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Bacterium ; + rdfs:subClassOf biolink:OrganismAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Bacterium . + owl:someValuesFrom biolink:OrganismAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalModifier ; + rdfs:subClassOf biolink:MacromolecularComplex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalModifier . + owl:someValuesFrom biolink:MacromolecularComplex . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysicalEntity ; + rdfs:subClassOf biolink:DatasetDistribution ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysicalEntity . + owl:someValuesFrom biolink:DatasetDistribution . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:StudyResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:StudyResult . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene_or_gene_product ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin . + owl:someValuesFrom biolink:GeneGroupingMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; + rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . + owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:LogOddsAnalysisResult ; + rdfs:subClassOf biolink:ReactionToCatalystAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LogOddsAnalysisResult . + owl:someValuesFrom biolink:ReactionToCatalystAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToGeneAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon_label ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MaterialSample ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon_label ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:in_taxon_label ] ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhysiologicalProcess ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysiologicalProcess . + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass . + owl:someValuesFrom biolink:PhysicalEssence . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + rdfs:subClassOf biolink:Device ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + owl:someValuesFrom biolink:Device . [] a owl:Restriction ; - rdfs:subClassOf biolink:Article ; + rdfs:subClassOf biolink:ChemicalRole ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Article . + owl:someValuesFrom biolink:ChemicalRole . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; + rdfs:subClassOf biolink:Book ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . + owl:someValuesFrom biolink:Book . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConceptCountAnalysisResult ; + rdfs:subClassOf biolink:DrugToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConceptCountAnalysisResult . + owl:someValuesFrom biolink:DrugToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; + rdfs:subClassOf biolink:CellularComponent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceFeatureRelationship . + owl:someValuesFrom biolink:CellularComponent . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity . + rdfs:subClassOf biolink:Cohort ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Cohort . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:StudyPopulation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:StudyPopulation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:MolecularEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:MolecularEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; + rdfs:subClassOf biolink:Article ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + owl:someValuesFrom biolink:Article . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; + rdfs:subClassOf biolink:RegulatoryRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . + owl:someValuesFrom biolink:RegulatoryRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralExposure ; + rdfs:subClassOf biolink:Mammal ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralExposure . + owl:someValuesFrom biolink:Mammal . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneExpressionMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:RegulatoryRegion ; + rdfs:subClassOf biolink:AccessibleDnaRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RegulatoryRegion . + owl:someValuesFrom biolink:AccessibleDnaRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + rdfs:subClassOf biolink:Plant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivity . + owl:someValuesFrom biolink:Plant . [] a owl:Restriction ; - rdfs:subClassOf biolink:PreprintPublication ; + rdfs:subClassOf biolink:PhenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PreprintPublication . + owl:someValuesFrom biolink:PhenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Activity ; + rdfs:subClassOf biolink:ExonToTranscriptRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Activity . + owl:someValuesFrom biolink:ExonToTranscriptRelationship . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineMixin . + rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Dataset ; + rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Dataset . + owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity . + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalMixture ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalMixture . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathognomonicityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:Case ; + rdfs:subClassOf biolink:DrugLabel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Case . + owl:someValuesFrom biolink:DrugLabel . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceAssociation ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceAssociation . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; + rdfs:subClassOf biolink:Phenomenon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . + owl:someValuesFrom biolink:Phenomenon . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProductIsoform ; + rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProductIsoform . + owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . + owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalIntervention ; + rdfs:subClassOf biolink:ClinicalFinding ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalIntervention . + owl:someValuesFrom biolink:ClinicalFinding . [] a owl:Restriction ; - rdfs:subClassOf biolink:AccessibleDnaRegion ; + rdfs:subClassOf biolink:SequenceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AccessibleDnaRegion . + owl:someValuesFrom biolink:SequenceAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathognomonicityQuantifier . + rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + rdfs:subClassOf biolink:GeographicLocationAtTime ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeographicLocationAtTime . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:SmallMolecule ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:SmallMolecule . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalEntity ; + rdfs:subClassOf biolink:ClinicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalEntity . + owl:someValuesFrom biolink:ClinicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalMeasurement ; + rdfs:subClassOf biolink:Procedure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalMeasurement . + owl:someValuesFrom biolink:Procedure . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:SensitivityQuantifier . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:minCardinality 0 ; + owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:synonym ] ; @@ -13695,95 +13580,29 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:GeneProductMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugLabel ; + rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugLabel . + owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalTrial ; + rdfs:subClassOf biolink:PopulationToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalTrial . + owl:someValuesFrom biolink:PopulationToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationToPopulationAssociation ; + rdfs:subClassOf biolink:PhysicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationToPopulationAssociation . + owl:someValuesFrom biolink:PhysicalEntity . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Case ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GrossAnatomicalStructure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GrossAnatomicalStructure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularComplex ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularComplex . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Drug ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Drug . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Behavior ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Behavior . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicExposure ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicExposure . + owl:someValuesFrom biolink:VariantToGeneAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; @@ -13791,485 +13610,460 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:TextMiningResult ; + rdfs:subClassOf biolink:ReagentTargetedGene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TextMiningResult . + owl:someValuesFrom biolink:ReagentTargetedGene . [] a owl:Restriction ; - rdfs:subClassOf biolink:Association ; + rdfs:subClassOf biolink:PosttranslationalModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Association . + owl:someValuesFrom biolink:PosttranslationalModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:Book ; + rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Book . + owl:someValuesFrom biolink:PathologicalAnatomicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Disease ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Disease . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; + rdfs:subClassOf biolink:Polypeptide ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneAssociation . + owl:someValuesFrom biolink:Polypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; + rdfs:subClassOf biolink:GeneToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + owl:someValuesFrom biolink:GeneToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFeature ; + rdfs:subClassOf biolink:BiologicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFeature . + owl:someValuesFrom biolink:BiologicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicBackgroundExposure ; + rdfs:subClassOf biolink:BehavioralExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicBackgroundExposure . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation . + owl:someValuesFrom biolink:BehavioralExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralFeature ; + rdfs:subClassOf biolink:GenomicSequenceLocalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralFeature . + owl:someValuesFrom biolink:GenomicSequenceLocalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; + rdfs:subClassOf biolink:PathologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NoncodingRNAProduct . + owl:someValuesFrom biolink:PathologicalProcess . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalProcess ; + rdfs:subClassOf biolink:EntityToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalProcess . + owl:someValuesFrom biolink:EntityToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGoTermAssociation ; + rdfs:subClassOf biolink:GeographicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGoTermAssociation . + owl:someValuesFrom biolink:GeographicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; + rdfs:subClassOf biolink:ClinicalCourse ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . + owl:someValuesFrom biolink:ClinicalCourse . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivity ; + rdfs:subClassOf biolink:RetrievalSource ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivity . + owl:someValuesFrom biolink:RetrievalSource . [] a owl:Restriction ; - rdfs:subClassOf biolink:SeverityValue ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SeverityValue . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Hospitalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Hospitalization . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin . + rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ChemicalToChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalAttribute ; + rdfs:subClassOf biolink:MicroRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalAttribute . + owl:someValuesFrom biolink:MicroRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:RetrievalSource ; + rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RetrievalSource . + owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntity ; + rdfs:subClassOf biolink:Genotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntity . + owl:someValuesFrom biolink:Genotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + rdfs:subClassOf biolink:SocioeconomicAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + owl:someValuesFrom biolink:SocioeconomicAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + rdfs:subClassOf biolink:CommonDataElement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToDiseaseAssociation . + owl:someValuesFrom biolink:CommonDataElement . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:Snv ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:Snv . [] a owl:Restriction ; - rdfs:subClassOf biolink:Virus ; + rdfs:subClassOf biolink:Activity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Virus . + owl:someValuesFrom biolink:Activity . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:in_taxon_label ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:in_taxon_label ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon_label ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalFinding ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalFinding . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + owl:someValuesFrom biolink:ThingWithTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:JournalArticle ; + rdfs:subClassOf biolink:ChemicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:JournalArticle . + owl:someValuesFrom biolink:ChemicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; + rdfs:subClassOf biolink:Protein ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Entity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Entity . + owl:someValuesFrom biolink:Protein . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Outcome ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicQuality ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicQuality . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Phenomenon ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Phenomenon . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGeneAssociation . + owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToVariantAssociation ; + rdfs:subClassOf biolink:EvidenceType ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToVariantAssociation . + owl:someValuesFrom biolink:EvidenceType . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocationAtTime ; + rdfs:subClassOf biolink:AnatomicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocationAtTime . + owl:someValuesFrom biolink:AnatomicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + rdfs:subClassOf biolink:GeneToGoTermAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . + owl:someValuesFrom biolink:GeneToGoTermAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Attribute ; + rdfs:subClassOf biolink:Dataset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Attribute . + owl:someValuesFrom biolink:Dataset . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToPathwayAssociation . + owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AdministrativeEntity ; + rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AdministrativeEntity . + owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Hospitalization ; + rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Hospitalization . + owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; + rdfs:subClassOf biolink:Association ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . + owl:someValuesFrom biolink:Association . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularEntity . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPathwayAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPathwayAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductIsoformMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneticInheritance ; + rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneticInheritance . + owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:frequency_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin . + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalExposure ; + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalExposure . + owl:someValuesFrom biolink:VariantToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntity ; + rdfs:subClassOf biolink:MolecularActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntity . + owl:someValuesFrom biolink:MolecularActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugExposure ; + rdfs:subClassOf biolink:Cell ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugExposure . + owl:someValuesFrom biolink:Cell . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalSex ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalSex . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior . + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToDiseaseAssociation . + owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cell ; + rdfs:subClassOf biolink:Case ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cell . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . + owl:someValuesFrom biolink:Case . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExonToTranscriptRelationship ; + rdfs:subClassOf biolink:GenotypeToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExonToTranscriptRelationship . + owl:someValuesFrom biolink:GenotypeToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + rdfs:subClassOf biolink:EnvironmentalFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismToOrganismAssociation . + owl:someValuesFrom biolink:EnvironmentalFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:EvidenceType ; + rdfs:subClassOf biolink:Serial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EvidenceType . + owl:someValuesFrom biolink:Serial . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genome ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genome . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EpigenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + rdfs:subClassOf biolink:Gene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + owl:someValuesFrom biolink:Gene . [] a owl:Restriction ; - rdfs:subClassOf biolink:Polypeptide ; + rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Polypeptide . + owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:InformationContentEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:InformationContentEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity . [] a owl:Restriction ; rdfs:subClassOf biolink:Exon ; @@ -14277,232 +14071,479 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Exon . [] a owl:Restriction ; - rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:ProcessedMaterial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . + owl:someValuesFrom biolink:ProcessedMaterial . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SeverityValue ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SeverityValue . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ProteinFamily ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ProteinFamily . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PathologicalProcessExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PathologicalProcessExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneFamily ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneFamily . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalModifier ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalModifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:NoncodingRNAProduct . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BookChapter ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BookChapter . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Transcript ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Transcript . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Onset ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Onset . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; + rdfs:subClassOf biolink:CellLine ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + owl:someValuesFrom biolink:CellLine . [] a owl:Restriction ; - rdfs:subClassOf biolink:Study ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Study . + owl:someValuesFrom biolink:ClinicalAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; + rdfs:subClassOf biolink:JournalArticle ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptionFactorBindingSite . + owl:someValuesFrom biolink:JournalArticle . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQualifierMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneticInheritance ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneticInheritance . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RNAProduct ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RNAProduct . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:object_specialization_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_specialization_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:disease_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:disease_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_specialization_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:disease_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_specialization_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:subject_specialization_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_specialization_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcessExposure ; + rdfs:subClassOf biolink:Human ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcessExposure . + owl:someValuesFrom biolink:Human . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinIsoform ; + rdfs:subClassOf biolink:Virus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinIsoform . + owl:someValuesFrom biolink:Virus . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Pathway ; + rdfs:subClassOf biolink:StudyVariable ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Pathway . + owl:someValuesFrom biolink:StudyVariable . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicSequenceLocalization ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicSequenceLocalization . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:Agent ; + rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Agent . + owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Invertebrate ; + rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Invertebrate . + owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_quotient ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_total ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_percentage ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_count ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EnvironmentalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EnvironmentalExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Vertebrate ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Vertebrate . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_percentage ] ; + owl:onProperty biolink:timepoint ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier . + owl:someValuesFrom biolink:ExposureEvent . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:RelationshipQuantifier . + owl:someValuesFrom biolink:SubjectOfInvestigation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypicSex ; + rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypicSex . + owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToGeneProductRelationship . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ] ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_quotient ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . + owl:someValuesFrom biolink:FrequencyQuantifier . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneAssociation . + owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Device ; + rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Device . + owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Mammal ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Mammal . + owl:someValuesFrom biolink:ReactionToParticipantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismAttribute ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismAttribute . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:FunctionalAssociation ; + rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FunctionalAssociation . + owl:someValuesFrom biolink:PathologicalAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; + rdfs:subClassOf biolink:TaxonToTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToParticipantAssociation . + owl:someValuesFrom biolink:TaxonToTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + owl:someValuesFrom biolink:BiologicalProcessOrActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptToGeneRelationship ; + rdfs:subClassOf biolink:Disease ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptToGeneRelationship . + owl:someValuesFrom biolink:Disease . [] a owl:Restriction ; rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; @@ -14510,59 +14551,54 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:ChiSquaredAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcess ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcess . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + rdfs:subClassOf biolink:Haplotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + owl:someValuesFrom biolink:Haplotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexChemicalExposure ; + rdfs:subClassOf biolink:ClinicalIntervention ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexChemicalExposure . + owl:someValuesFrom biolink:ClinicalIntervention . [] a owl:Restriction ; - rdfs:subClassOf biolink:Patent ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Patent . + owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Event ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Event . + owl:someValuesFrom biolink:SequenceFeatureRelationship . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . diff --git a/project/protobuf/biolink_model.proto b/project/protobuf/biolink_model.proto index e7d11f0e1..1d81095ed 100644 --- a/project/protobuf/biolink_model.proto +++ b/project/protobuf/biolink_model.proto @@ -339,6 +339,9 @@ message BehaviorToBehavioralFeatureAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -584,6 +587,9 @@ message CaseToPhenotypicFeatureAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -636,6 +642,9 @@ message CausalGeneToDiseaseAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -1108,7 +1117,7 @@ message ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation fDAIDAAdverseEventEnum fDAAdverseEventLevel = 0 predicateType predicate = 0 } -// This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect. +// This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is a secondary undesirable effect. message ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation { string id = 0 @@ -1734,6 +1743,9 @@ message CorrelatedGeneToDiseaseAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -2099,6 +2111,9 @@ message DiseaseToPhenotypicFeatureAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 } // A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease message Drug @@ -2280,6 +2295,9 @@ message DruggableGeneToDiseaseAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -2639,6 +2657,9 @@ message ExposureEventToPhenotypicFeatureAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -2876,6 +2897,9 @@ message GeneAsAModelOfDiseaseAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -2948,6 +2972,9 @@ message GeneHasVariantThatContributesToDiseaseAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -3051,6 +3078,9 @@ message GeneToDiseaseAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -3107,6 +3137,9 @@ message GeneToDiseaseOrPhenotypicFeatureAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -3465,6 +3498,9 @@ message GeneToPhenotypicFeatureAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -3833,6 +3869,9 @@ message GenotypeToPhenotypicFeatureAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 @@ -5401,6 +5440,9 @@ message PhenotypicFeatureToPhenotypicFeatureAssociation double hasQuotient = 0 double hasPercentage = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 } // A property of a phenotype message PhenotypicQuality @@ -6766,6 +6808,9 @@ message VariantToPhenotypicFeatureAssociation string qualifiedPredicate = 0 biologicalSex sexQualifier = 0 disease diseaseContextQualifier = 0 + uriorcurie subjectSpecializationQualifier = 0 + uriorcurie objectSpecializationQualifier = 0 + string anatomicalContextQualifier = 0 integer hasCount = 0 integer hasTotal = 0 double hasQuotient = 0 diff --git a/project/shacl/biolink_model.shacl.ttl b/project/shacl/biolink_model.shacl.ttl index 459173163..e4e842c9f 100644 --- a/project/shacl/biolink_model.shacl.ttl +++ b/project/shacl/biolink_model.shacl.ttl @@ -10,39 +10,43 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -50,72 +54,74 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:order 9 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ] ; + sh:order 4 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:AccessibleDnaRegion . biolink:Activity a sh:NodeShape ; sh:closed true ; sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -123,38 +129,33 @@ biolink:Activity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -162,11 +163,10 @@ biolink:Activity a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ] ; + sh:order 3 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; @@ -177,51 +177,47 @@ biolink:ActivityAndBehavior a sh:NodeShape ; biolink:AdministrativeEntity a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( biolink:affiliation rdf:type biolink:address ) ; + sh:ignoredProperties ( biolink:address rdf:type biolink:affiliation ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -229,292 +225,293 @@ biolink:AdministrativeEntity a sh:NodeShape ; sh:order 9 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -522,326 +519,272 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at an earlier time" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at a later time" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the part" ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -849,50 +792,17 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:AnatomicalEntity ; sh:description "the whole" ; sh:maxCount 1 ; @@ -900,129 +810,206 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . - -biolink:Annotation a sh:NodeShape ; - sh:closed false ; - sh:description "Biolink Model root class for entity annotations." ; - sh:ignoredProperties ( biolink:has_numeric_value biolink:has_unit rdf:type ) ; - sh:targetClass biolink:Annotation . - -biolink:Article a sh:NodeShape ; - sh:closed true ; - sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:issue ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the part" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + +biolink:Annotation a sh:NodeShape ; + sh:closed false ; + sh:description "Biolink Model root class for entity annotations." ; + sh:ignoredProperties ( biolink:has_unit biolink:has_numeric_value rdf:type ) ; + sh:targetClass biolink:Annotation . + +biolink:Article a sh:NodeShape ; + sh:closed true ; + sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:format ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:creation_date ], + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:order 12 ; + sh:path biolink:rights ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdfs:label ], + sh:order 25 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:deprecated ], + sh:order 19 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path dct:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; @@ -1030,346 +1017,335 @@ biolink:Article a sh:NodeShape ; sh:order 1 ; sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:order 18 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:rights ], + sh:order 11 ; + sh:path biolink:license ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:creation_date ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:issue ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:type ], + sh:order 8 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:volume ] ; + sh:path biolink:category ] ; sh:targetClass biolink:Article . biolink:Association a sh:NodeShape ; sh:closed true ; sh:description "A typed association between two entities, supported by evidence" ; - sh:ignoredProperties ( biolink:subject_direction_qualifier biolink:reaction_side biolink:temporal_context_qualifier biolink:sex_qualifier biolink:species_context_qualifier biolink:anatomical_context_qualifier biolink:subject_aspect_qualifier biolink:reaction_direction biolink:object_form_or_variant_qualifier biolink:strand biolink:onset_qualifier biolink:disease_context_qualifier biolink:has_total biolink:subject_derivative_qualifier biolink:object_direction_qualifier biolink:subject_form_or_variant_qualifier biolink:clinical_approval_status biolink:object_derivative_qualifier biolink:subject_context_qualifier biolink:has_count biolink:catalyst_qualifier biolink:start_interbase_coordinate biolink:stage_qualifier biolink:phenotypic_state biolink:quantifier_qualifier biolink:stoichiometry biolink:subject_part_qualifier biolink:qualified_predicate biolink:has_percentage biolink:max_research_phase biolink:object_aspect_qualifier biolink:associated_environmental_context biolink:phase biolink:FDA_adverse_event_level biolink:interacting_molecules_category biolink:frequency_qualifier biolink:population_context_qualifier biolink:object_part_qualifier biolink:expression_site biolink:end_interbase_coordinate biolink:has_quotient biolink:object_context_qualifier biolink:genome_build biolink:causal_mechanism_qualifier rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:ignoredProperties ( biolink:has_total biolink:object_specialization_qualifier biolink:anatomical_context_qualifier biolink:object_derivative_qualifier rdf:type biolink:quantifier_qualifier biolink:object_context_qualifier biolink:catalyst_qualifier biolink:population_context_qualifier biolink:stoichiometry biolink:temporal_context_qualifier biolink:strand biolink:expression_site biolink:associated_environmental_context biolink:subject_direction_qualifier biolink:subject_aspect_qualifier biolink:has_count biolink:frequency_qualifier biolink:interacting_molecules_category biolink:reaction_direction biolink:reaction_side biolink:phenotypic_state biolink:object_part_qualifier biolink:start_interbase_coordinate biolink:subject_derivative_qualifier biolink:onset_qualifier biolink:clinical_approval_status biolink:object_form_or_variant_qualifier biolink:causal_mechanism_qualifier biolink:has_percentage biolink:phase biolink:sex_qualifier biolink:species_context_qualifier biolink:object_direction_qualifier biolink:object_aspect_qualifier biolink:subject_part_qualifier biolink:has_quotient biolink:subject_form_or_variant_qualifier biolink:end_interbase_coordinate biolink:stage_qualifier biolink:disease_context_qualifier biolink:qualified_predicate biolink:max_research_phase biolink:subject_specialization_qualifier biolink:subject_context_qualifier biolink:FDA_adverse_event_level biolink:genome_build ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ] ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:Association . biolink:Bacterium a sh:NodeShape ; sh:closed true ; sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -1377,425 +1353,467 @@ biolink:Bacterium a sh:NodeShape ; sh:order 4 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:Bacterium . biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:BehavioralFeature ; + sh:description "behavioral feature that is the object of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 44 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 40 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 49 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:object_specialization_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 50 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 22 ; sh:path biolink:subject_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; + sh:order 31 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:BehavioralFeature ; - sh:description "behavioral feature that is the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 29 ; sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:path biolink:subject_specialization_qualifier ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 16 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 46 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; + sh:order 53 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 39 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:double ; + sh:order 41 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; + sh:order 45 ; sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 37 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 36 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 51 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 48 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:sex_qualifier ] ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . biolink:BehavioralExposure a sh:NodeShape ; sh:closed true ; sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ] ; + sh:path biolink:xref ] ; sh:targetClass biolink:BehavioralExposure . biolink:BehavioralOutcome a sh:NodeShape ; @@ -1806,149 +1824,139 @@ biolink:BehavioralOutcome a sh:NodeShape ; biolink:BiologicalEntity a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( biolink:has_input biolink:enabled_by biolink:has_gene biolink:has_biological_sequence biolink:symbol biolink:has_gene_or_gene_product biolink:has_zygosity biolink:has_output rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:ignoredProperties ( biolink:enabled_by rdf:type biolink:has_input biolink:has_gene_or_gene_product biolink:has_biological_sequence biolink:has_gene biolink:has_output biolink:symbol biolink:has_zygosity ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:BiologicalEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:closed true ; sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_output ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_input ], + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:order 0 ; + sh:path biolink:has_input ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -1956,6 +1964,17 @@ biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -1967,35 +1986,29 @@ biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:enabled_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:BiologicalProcessOrActivity . biolink:BioticExposure a sh:NodeShape ; sh:closed true ; sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -2007,28 +2020,34 @@ biolink:BioticExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -2036,69 +2055,92 @@ biolink:BioticExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ] ; + sh:order 10 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:BioticExposure . biolink:Book a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -2106,78 +2148,54 @@ biolink:Book a sh:NodeShape ; sh:order 10 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'book'." ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; @@ -2186,113 +2204,117 @@ biolink:Book a sh:NodeShape ; sh:order 14 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ] ; + sh:order 18 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Book . biolink:BookChapter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 15 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:summary ], + sh:order 11 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "chapter of a book" ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:chapter ], + sh:order 9 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], + sh:order 4 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:volume ], - [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], + sh:order 19 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:license ], + sh:order 12 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:volume ], [ sh:datatype xsd:anyURI ; sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; sh:maxCount 1 ; @@ -2300,71 +2322,67 @@ biolink:BookChapter a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:published_in ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:keywords ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:type ], + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "chapter of a book" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:chapter ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:mesh_terms ] ; + sh:order 22 ; + sh:path dct:description ] ; sh:targetClass biolink:BookChapter . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An abstract association for use where the case is the subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -2372,13 +2390,13 @@ biolink:CaseToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:CaseToEntityAssociationMixin . biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -2386,189 +2404,149 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 6 ; + sh:path biolink:object_specialization_qualifier ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 38 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 27 ; + sh:order 30 ; sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 20 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 45 ; + sh:path biolink:has_total ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 49 ; - sh:path biolink:qualified_predicate ], + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 32 ; + sh:order 35 ; sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 23 ; sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 51 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 46 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Case ; sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; @@ -2576,53 +2554,75 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; - sh:path biolink:id ], + sh:path biolink:p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; + sh:order 53 ; sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:negated ], + sh:path biolink:subject_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 48 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -2630,40 +2630,59 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 27 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 36 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], + sh:order 40 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -2675,342 +2694,377 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ] ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:object_aspect_qualifier ] ; sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:has_total ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 6 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 48 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 39 ; + sh:path biolink:iri ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], + sh:order 26 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 42 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 50 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], + sh:order 12 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 15 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; + sh:order 51 ; sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 29 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 20 ; sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 25 ; + sh:path biolink:object_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 31 ; + sh:order 34 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 22 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 10 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 46 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; sh:order 41 ; - sh:path biolink:has_attribute ], + sh:path rdf:type ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 32 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:qualifiers ], + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 36 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:order 52 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:object_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_evidence ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], + sh:order 30 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 21 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], + sh:order 31 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 49 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:path biolink:object_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 13 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], + sh:order 45 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 24 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 43 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ] ; + sh:order 38 ; + sh:path biolink:id ] ; sh:targetClass biolink:CausalGeneToDiseaseAssociation . biolink:Cell a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -3018,209 +3072,100 @@ biolink:Cell a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Cell . biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -3234,201 +3179,232 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . - -biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; - sh:ignoredProperties ( biolink:object_aspect_qualifier biolink:subject_direction_qualifier biolink:object_direction_qualifier biolink:subject_aspect_qualifier biolink:frequency_qualifier biolink:qualified_predicate rdf:type ) ; - sh:property [ sh:datatype xsd:float ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ] ; + sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + +biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + sh:ignoredProperties ( rdf:type biolink:subject_direction_qualifier biolink:qualified_predicate biolink:subject_aspect_qualifier biolink:frequency_qualifier biolink:object_direction_qualifier biolink:object_aspect_qualifier ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -3436,48 +3412,91 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -3485,68 +3504,103 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 36 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; @@ -3560,160 +3614,175 @@ biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:CellLine ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:CellLine ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:CellLineToEntityAssociationMixin . biolink:CellularOrganism a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:CellularOrganism . biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 53 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:object_category_closure ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:timepoint ], + sh:order 50 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:qualifier ], + sh:order 47 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 52 ; + sh:path biolink:has_attribute ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:object_namespace ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 49 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:publications ], + sh:order 14 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -3727,116 +3796,32 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 17 ; sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdfs:label ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:agent_type ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:negated ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:iri ], [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:in ( "metabolite" ) ; sh:maxCount 1 ; @@ -3847,334 +3832,282 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:order 10 ; sh:path biolink:object_direction_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_closure ], + sh:order 40 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:AnatomicalEntity ; sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 34 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:predicate ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 19 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], + sh:order 21 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:subject_namespace ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 16 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 52 ; - sh:path biolink:has_attribute ], + sh:order 32 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdf:type ], + sh:order 51 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:id ], + sh:order 29 ; + sh:path biolink:original_subject ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path rdf:subject ], [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:object_form_or_variant_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; + sh:order 45 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 24 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 43 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 35 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . + +biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -4182,160 +4115,200 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . - -biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A regulatory relationship between two genes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 28 ; sh:path biolink:p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:GeneOrGeneProduct ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 34 ; sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . + +biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A regulatory relationship between two genes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 37 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -4343,65 +4316,64 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:nodeKind sh:BlankNodeOrIRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "the direction is always from regulator to regulated" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 35 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; @@ -4411,22 +4383,104 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "the direction is always from regulator to regulated" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ] ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ] ; sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; @@ -4446,20 +4500,20 @@ biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . biolink:ChemicalExposure a sh:NodeShape ; @@ -4467,84 +4521,55 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:description "A chemical exposure is an intake of a particular chemical entity." ; sh:ignoredProperties ( biolink:has_gene_or_gene_product rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:timepoint ], + sh:order 2 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -4552,167 +4577,129 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ChemicalExposure . - -biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:subject_part_qualifier ], + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; + sh:order 11 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; + sh:order 6 ; sh:path biolink:id ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ] ; + sh:targetClass biolink:ChemicalExposure . + +biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 45 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:knowledge_source ], + sh:order 41 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 10 ; - sh:path rdf:object ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], + sh:order 26 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 46 ; + sh:path biolink:deprecated ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:agent_type ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], + sh:order 8 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 39 ; + sh:path biolink:id ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 12 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], + sh:order 14 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -4720,233 +4707,300 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:order 31 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path rdfs:label ], + sh:order 37 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 38 ; + sh:path biolink:has_supporting_studies ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:object_part_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:predicate ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], + sh:order 30 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:original_predicate ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:order 24 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:subject ], + sh:order 20 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:ChemicalGeneInteractionAssociation . - -biolink:ChemicalMixture a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:order 11 ; + sh:path biolink:negated ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:subject_context_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 40 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 10 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:order 18 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], + sh:order 28 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:order 43 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 22 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], + sh:order 21 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:ChemicalGeneInteractionAssociation . + +biolink:ChemicalMixture a sh:NodeShape ; + sh:closed true ; + sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ] ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ] ; sh:targetClass biolink:ChemicalMixture . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; @@ -4958,35 +5012,100 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:closed true ; sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:FDA_adverse_event_level ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -4994,60 +5113,44 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:order 39 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 3 ; + sh:path biolink:FDA_adverse_event_level ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -5055,69 +5158,48 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:iri ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -5125,17 +5207,6 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -5148,11 +5219,6 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -5160,137 +5226,102 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:order 36 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ] ; + sh:order 6 ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; + sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is a secondary undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:iri ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; @@ -5306,97 +5337,91 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:timepoint ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -5404,52 +5429,118 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:order 37 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalToChemicalAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; - sh:ignoredProperties ( biolink:reaction_side biolink:catalyst_qualifier biolink:reaction_direction biolink:stoichiometry rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 36 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 19 ; sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + +biolink:ChemicalToChemicalAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; + sh:ignoredProperties ( rdf:type biolink:reaction_side biolink:catalyst_qualifier biolink:reaction_direction biolink:stoichiometry ) ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -5457,11 +5548,19 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -5469,249 +5568,192 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:ChemicalToChemicalAssociation . biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:closed true ; sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:catalyst_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -5719,65 +5761,63 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 35 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 32 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the downstream chemical entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:ChemicalEntity ; sh:description "the upstream chemical entity" ; sh:maxCount 1 ; @@ -5785,34 +5825,71 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -5820,104 +5897,62 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ] ; + sh:order 39 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -5925,193 +5960,212 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "the disease or phenotype that is affected by the chemical" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ] ; + sh:order 3 ; + sh:path biolink:negated ] ; sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; @@ -6125,31 +6179,60 @@ biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:ChemicalToEntityAssociationMixin . biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -6158,60 +6241,39 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6219,181 +6281,172 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that is affected by the chemical" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ] ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ] ; sh:targetClass biolink:ChemicalToPathwayAssociation . biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -6401,104 +6454,119 @@ biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:order 6 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:order 3 ; + sh:path biolink:creation_date ] ; sh:targetClass biolink:ChiSquaredAnalysisResult . biolink:ClinicalCourse a sh:NodeShape ; sh:closed true ; sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -6511,78 +6579,74 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:ClinicalCourse . + +biolink:ClinicalEntity a sh:NodeShape ; + sh:closed true ; + sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 9 ; sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:ClinicalCourse . - -biolink:ClinicalEntity a sh:NodeShape ; - sh:closed true ; - sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6590,31 +6654,15 @@ biolink:ClinicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -6622,10 +6670,16 @@ biolink:ClinicalEntity a sh:NodeShape ; sh:order 2 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ] ; sh:targetClass biolink:ClinicalEntity . biolink:ClinicalFinding a sh:NodeShape ; @@ -6633,168 +6687,167 @@ biolink:ClinicalFinding a sh:NodeShape ; sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:class biolink:ClinicalAttribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:class biolink:ClinicalAttribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ClinicalFinding . biolink:ClinicalIntervention a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ClinicalIntervention . biolink:ClinicalMeasurement a sh:NodeShape ; sh:closed true ; sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; @@ -6804,12 +6857,36 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -6818,61 +6895,38 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:order 1 ; sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; + sh:path biolink:xref ] ; sh:targetClass biolink:ClinicalMeasurement . biolink:ClinicalModifier a sh:NodeShape ; @@ -6880,24 +6934,18 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; @@ -6919,6 +6967,17 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -6930,17 +6989,13 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -6954,42 +7009,25 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:ClinicalModifier . biolink:ClinicalTrial a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -7001,17 +7039,17 @@ biolink:ClinicalTrial a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -7019,11 +7057,11 @@ biolink:ClinicalTrial a sh:NodeShape ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -7035,29 +7073,45 @@ biolink:ClinicalTrial a sh:NodeShape ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:ClinicalTrial . biolink:CodingSequence a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -7065,66 +7119,66 @@ biolink:CodingSequence a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ] ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:CodingSequence . biolink:Cohort a sh:NodeShape ; @@ -7132,56 +7186,48 @@ biolink:Cohort a sh:NodeShape ; sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; @@ -7192,23 +7238,31 @@ biolink:Cohort a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Cohort . biolink:CommonDataElement a sh:NodeShape ; @@ -7216,6 +7270,32 @@ biolink:CommonDataElement a sh:NodeShape ; sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; @@ -7226,15 +7306,16 @@ biolink:CommonDataElement a sh:NodeShape ; sh:order 5 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -7245,41 +7326,12 @@ biolink:CommonDataElement a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -7294,33 +7346,34 @@ biolink:CommonDataElement a sh:NodeShape ; sh:order 6 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:CommonDataElement . biolink:ComplexChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -7328,54 +7381,56 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:order 4 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -7383,11 +7438,10 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -7400,31 +7454,56 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "" ; + sh:property [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; @@ -7437,215 +7516,184 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:is_supplement ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ] ; + sh:path biolink:routes_of_delivery ] ; sh:targetClass biolink:ComplexMolecularMixture . biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ] ; sh:targetClass biolink:ConceptCountAnalysisResult . biolink:ConfidenceLevel a sh:NodeShape ; sh:closed true ; sh:description "Level of confidence in a statement" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -7653,23 +7701,31 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 3 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -7677,19 +7733,18 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 12 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -7697,150 +7752,198 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 13 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:ConfidenceLevel . biolink:ContributorAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:InformationContentEntity ; - sh:description "information content entity which an agent has helped realise" ; + [ sh:class biolink:Agent ; + sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -7848,385 +7951,354 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:InformationContentEntity ; + sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 26 ; + sh:path biolink:object_label_closure ] ; + sh:targetClass biolink:ContributorAssociation . + +biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 23 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 45 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 32 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 39 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to correlate with the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:timepoint ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 34 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; - sh:targetClass biolink:ContributorAssociation . - -biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 33 ; + sh:path biolink:object_label_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 42 ; + sh:path rdfs:label ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:path biolink:object_category ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 38 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 27 ; + sh:path biolink:object_closure ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 47 ; + sh:order 50 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 41 ; + sh:path rdf:type ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; + sh:order 53 ; sh:path biolink:frequency_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to correlate with the disease." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 9 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 24 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 36 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:path biolink:has_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 11 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:double ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], + sh:order 21 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], + sh:order 43 ; + sh:path dct:description ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 11 ; + sh:order 14 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:order 52 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 40 ; + sh:path biolink:category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:p_value ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 47 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 30 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ] ; + sh:order 22 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:has_quotient ] ; sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . biolink:DatasetSummary a sh:NodeShape ; @@ -8234,84 +8306,65 @@ biolink:DatasetSummary a sh:NodeShape ; sh:description "an item that holds summary level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:source_web_page ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:rights ], + sh:order 0 ; + sh:path biolink:source_web_page ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path schema1:logo ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -8319,18 +8372,37 @@ biolink:DatasetSummary a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:creation_date ] ; + sh:order 1 ; + sh:path schema1:logo ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ] ; sh:targetClass biolink:DatasetSummary . biolink:DatasetVersion a sh:NodeShape ; @@ -8338,48 +8410,25 @@ biolink:DatasetVersion a sh:NodeShape ; sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:ingest_date ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdf:type ], + [ sh:class biolink:Dataset ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_dataset ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -8391,55 +8440,78 @@ biolink:DatasetVersion a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:creation_date ], + sh:order 12 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:class biolink:DatasetDistribution ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path dct:distribution ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:ingest_date ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:category ], - [ sh:class biolink:Dataset ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_dataset ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:DatasetVersion . biolink:DiagnosticAid a sh:NodeShape ; @@ -8447,22 +8519,11 @@ biolink:DiagnosticAid a sh:NodeShape ; sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -8470,89 +8531,95 @@ biolink:DiagnosticAid a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:DiagnosticAid . - -biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 9 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ] ; + sh:targetClass biolink:DiagnosticAid . + +biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -8560,56 +8627,61 @@ biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ] ; + sh:order 0 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; @@ -8621,20 +8693,20 @@ biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -8648,29 +8720,17 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:closed true ; sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -8683,251 +8743,251 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:GeneticInheritance ; + sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:GeneticInheritance ; - sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -8935,27 +8995,23 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -8963,156 +9019,165 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:order 35 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + sh:order 22 ; + sh:path biolink:object_category_closure ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Disease ; + sh:property [ sh:class biolink:Disease ; sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -9125,52 +9190,86 @@ biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:DiseaseToEntityAssociationMixin . biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an exposure event and a disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:Disease ; + sh:description "disease class" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:ExposureEvent ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9183,154 +9282,140 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -9338,23 +9423,10 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:order 20 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:DiseaseToExposureEventAssociation . biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -9362,79 +9434,80 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 33 ; + sh:path biolink:subject_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:p_value ], + sh:order 54 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 14 ; sh:path biolink:qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:timepoint ], + sh:order 18 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 46 ; + sh:path dct:description ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 22 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:onset_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 21 ; - sh:path biolink:original_subject ], + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -9442,246 +9515,302 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 10 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:object_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; sh:order 50 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_evidence ], + sh:order 9 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 35 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 2 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 19 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:object_label_closure ], + sh:order 1 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 40 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 52 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sex_qualifier ], + sh:order 7 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 26 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:category ], + sh:order 20 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:iri ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_total ], + sh:order 25 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; + sh:order 49 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], + sh:order 17 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; + sh:order 48 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_quotient ], + sh:order 13 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:id ], + sh:order 36 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path rdfs:label ], + sh:order 24 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 27 ; sh:path biolink:subject_category ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:onset_qualifier ], + sh:order 16 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_closure ], + sh:order 53 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 42 ; + sh:path biolink:iri ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:has_percentage ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:negated ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 39 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 31 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 34 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:publications ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 37 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:frequency_qualifier ] ; + sh:order 12 ; + sh:path biolink:anatomical_context_qualifier ] ; sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . biolink:DrugExposure a sh:NodeShape ; sh:closed true ; sh:description "A drug exposure is an intake of a particular drug." ; sh:ignoredProperties ( biolink:has_gene_or_gene_product rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -9694,116 +9823,94 @@ biolink:DrugExposure a sh:NodeShape ; sh:order 10 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_attribute_type ], + sh:path biolink:has_attribute_type ] ; + sh:targetClass biolink:DrugExposure . + +biolink:DrugLabel a sh:NodeShape ; + sh:closed true ; + sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path rdf:type ], + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 5 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 14 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:DrugExposure . - -biolink:DrugLabel a sh:NodeShape ; - sh:closed true ; - sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:mesh_terms ], @@ -9813,82 +9920,72 @@ biolink:DrugLabel a sh:NodeShape ; sh:order 7 ; sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 16 ; + sh:path biolink:category ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ] ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An interaction between a drug and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -9901,14 +9998,7 @@ biolink:DrugToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:predicate ] ; sh:targetClass biolink:DrugToEntityAssociationMixin . biolink:DrugToGeneAssociation a sh:NodeShape ; @@ -9916,27 +10006,46 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:Drug ; sh:description "the drug that is an interactor" ; sh:maxCount 1 ; @@ -9944,12 +10053,16 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -9957,92 +10070,93 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; @@ -10050,45 +10164,47 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -10100,44 +10216,18 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ] ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:DrugToGeneAssociation . biolink:DrugToGeneInteractionExposure a sh:NodeShape ; @@ -10150,360 +10240,284 @@ biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:timepoint ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:full_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_qualitative_value ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:synonym ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:timepoint ], + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:iri ] ; + sh:order 10 ; + sh:path biolink:full_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 46 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 45 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 10 ; + sh:path biolink:negated ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; + sh:order 33 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:sex_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; + sh:order 53 ; sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 34 ; + sh:order 37 ; sh:path biolink:has_supporting_studies ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:order 19 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:has_attribute ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:description "connects an association to an instance of supporting evidence" ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 48 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 22 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 38 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:double ; + sh:order 35 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 26 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:order 9 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:publications ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 8 ; + sh:path biolink:object_specialization_qualifier ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -10511,11 +10525,6 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -10527,291 +10536,275 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; + sh:order 30 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:DruggableGeneToDiseaseAssociation . - -biolink:Entity a sh:NodeShape ; - sh:closed false ; - sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; - sh:ignoredProperties ( biolink:upstream_resource_ids biolink:authors biolink:temporal_context_qualifier biolink:species_context_qualifier biolink:trade_name biolink:object_form_or_variant_qualifier biolink:routes_of_delivery biolink:onset_qualifier biolink:has_supporting_studies biolink:strand biolink:original_predicate biolink:provided_by biolink:subject_form_or_variant_qualifier biolink:clinical_approval_status biolink:has_evidence biolink:phenotypic_state biolink:max_research_phase biolink:has_biological_sequence biolink:license biolink:FDA_adverse_event_level biolink:available_from biolink:summary biolink:ingest_date biolink:subject_category_closure biolink:has_gene biolink:has_procedure biolink:iso_abbreviation biolink:object_closure rdf:type biolink:subject_closure biolink:highest_FDA_approval_status biolink:subject_category biolink:has_attribute_type biolink:has_total biolink:in_taxon biolink:object_namespace biolink:max_tolerated_dose biolink:has_count biolink:knowledge_source biolink:affiliation biolink:qualifiers biolink:enabled_by biolink:chapter biolink:p_value biolink:has_gene_or_gene_product biolink:primary_knowledge_source biolink:resource_role biolink:volume biolink:has_input rdf:predicate biolink:object_category_closure biolink:population_context_qualifier biolink:object_part_qualifier biolink:is_toxic biolink:original_subject rdf:subject biolink:retrieval_source_ids biolink:subject_namespace biolink:creation_date biolink:reaction_side biolink:sex_qualifier biolink:anatomical_context_qualifier biolink:format biolink:has_output biolink:mesh_terms schema1:logo biolink:has_quantitative_value biolink:issue biolink:object_direction_qualifier dct:distribution biolink:subject_context_qualifier biolink:catalyst_qualifier biolink:stage_qualifier biolink:quantifier_qualifier biolink:stoichiometry biolink:subject_part_qualifier biolink:agent_type biolink:has_percentage biolink:in_taxon_label biolink:synonym biolink:publications biolink:phase biolink:timepoint biolink:pages biolink:is_metabolite biolink:has_drug biolink:symbol biolink:longitude biolink:causal_mechanism_qualifier dct:type biolink:object_label_closure biolink:published_in biolink:has_chemical_role biolink:subject_direction_qualifier biolink:knowledge_level biolink:rights biolink:object_category biolink:subject_aspect_qualifier biolink:adjusted_p_value biolink:reaction_direction biolink:disease_context_qualifier biolink:latitude biolink:subject_label_closure biolink:aggregator_knowledge_source biolink:original_object biolink:subject_derivative_qualifier biolink:qualifier biolink:object_derivative_qualifier biolink:start_interbase_coordinate biolink:qualified_predicate rdf:object biolink:has_qualitative_value biolink:is_supplement biolink:object_aspect_qualifier biolink:resource_id biolink:source_web_page biolink:associated_environmental_context biolink:has_dataset biolink:address biolink:interacting_molecules_category biolink:frequency_qualifier biolink:drug_regulatory_status_world_wide biolink:keywords biolink:has_taxonomic_rank biolink:expression_site biolink:xref biolink:end_interbase_coordinate biolink:has_quotient biolink:full_name biolink:has_device biolink:negated biolink:has_zygosity biolink:object_context_qualifier biolink:distribution_download_url biolink:genome_build ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:deprecated ], + sh:order 20 ; + sh:path biolink:timepoint ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:category ], + sh:order 52 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 31 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 43 ; sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 42 ; sh:path rdfs:label ], + [ sh:description "connects an association to an instance of supporting evidence" ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:order 14 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Entity . - -biolink:EntityToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 21 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 41 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; + sh:order 23 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 39 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 40 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 17 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 28 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 50 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 49 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 36 ; + sh:path biolink:adjusted_p_value ] ; + sh:targetClass biolink:DruggableGeneToDiseaseAssociation . + +biolink:Entity a sh:NodeShape ; + sh:closed false ; + sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; + sh:ignoredProperties ( biolink:chapter biolink:object_specialization_qualifier biolink:has_device biolink:agent_type biolink:object_context_qualifier biolink:synonym dct:distribution dct:type biolink:trade_name biolink:object_category biolink:format biolink:qualifiers biolink:subject_direction_qualifier biolink:xref biolink:aggregator_knowledge_source biolink:frequency_qualifier biolink:original_subject biolink:subject_derivative_qualifier biolink:summary biolink:subject_label_closure biolink:resource_id biolink:publications biolink:volume biolink:subject_part_qualifier biolink:creation_date biolink:stage_qualifier biolink:has_procedure biolink:max_research_phase biolink:has_gene biolink:genome_build biolink:anatomical_context_qualifier biolink:issue biolink:quantifier_qualifier biolink:has_evidence biolink:address biolink:has_attribute_type biolink:authors biolink:stoichiometry biolink:has_output biolink:has_qualitative_value biolink:temporal_context_qualifier biolink:expression_site biolink:associated_environmental_context biolink:is_metabolite biolink:has_input biolink:full_name biolink:reaction_side biolink:license biolink:adjusted_p_value biolink:has_zygosity biolink:qualifier biolink:onset_qualifier biolink:clinical_approval_status biolink:object_category_closure biolink:has_gene_or_gene_product biolink:subject_category_closure biolink:has_dataset biolink:sex_qualifier biolink:primary_knowledge_source biolink:object_direction_qualifier biolink:object_aspect_qualifier biolink:is_toxic biolink:iso_abbreviation biolink:highest_FDA_approval_status biolink:retrieval_source_ids biolink:qualified_predicate biolink:source_web_page biolink:has_drug biolink:subject_specialization_qualifier biolink:drug_regulatory_status_world_wide biolink:FDA_adverse_event_level biolink:subject_context_qualifier biolink:ingest_date biolink:has_chemical_role biolink:timepoint biolink:catalyst_qualifier biolink:upstream_resource_ids biolink:routes_of_delivery biolink:object_label_closure rdf:subject biolink:enabled_by biolink:subject_aspect_qualifier biolink:has_biological_sequence schema1:logo biolink:reaction_direction biolink:pages biolink:start_interbase_coordinate biolink:object_form_or_variant_qualifier biolink:max_tolerated_dose biolink:keywords biolink:has_percentage biolink:phase biolink:species_context_qualifier biolink:is_supplement biolink:subject_form_or_variant_qualifier biolink:end_interbase_coordinate biolink:available_from biolink:p_value biolink:object_namespace rdf:predicate biolink:knowledge_level biolink:subject_category biolink:symbol biolink:affiliation rdf:object biolink:subject_namespace biolink:has_total biolink:rights rdf:type biolink:object_derivative_qualifier biolink:has_supporting_studies biolink:population_context_qualifier biolink:negated biolink:strand biolink:object_closure biolink:has_quantitative_value biolink:published_in biolink:provided_by biolink:longitude biolink:has_count biolink:interacting_molecules_category biolink:original_predicate biolink:phenotypic_state biolink:object_part_qualifier biolink:latitude biolink:causal_mechanism_qualifier biolink:has_taxonomic_rank biolink:knowledge_source biolink:in_taxon biolink:resource_role biolink:distribution_download_url biolink:has_quotient biolink:original_object biolink:subject_closure biolink:disease_context_qualifier biolink:in_taxon_label biolink:mesh_terms ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:order 4 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 5 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 2 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; + sh:order 7 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 1 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:Entity . + +biolink:EntityToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:order 24 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10819,10 +10812,125 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:max_research_phase ] ; + sh:path biolink:max_research_phase ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:EntityToDiseaseAssociation . biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; @@ -10830,11 +10938,11 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:description "mixin class for any association whose object (target node) is a disease" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; @@ -10847,55 +10955,55 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ] ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -10903,13 +11011,13 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; @@ -10942,14 +11050,13 @@ biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for entity to disease or phenotype associations." ; - sh:ignoredProperties ( biolink:has_percentage biolink:has_quotient biolink:sex_qualifier biolink:has_count biolink:disease_context_qualifier rdf:type biolink:has_total ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:ignoredProperties ( biolink:has_total biolink:anatomical_context_qualifier biolink:object_specialization_qualifier biolink:disease_context_qualifier rdf:type biolink:has_count biolink:has_percentage biolink:subject_specialization_qualifier biolink:sex_qualifier biolink:has_quotient ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10957,11 +11064,13 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -10969,29 +11078,28 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; @@ -11030,217 +11138,225 @@ biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 22 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:order 0 ; + sh:path biolink:clinical_approval_status ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 38 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:max_research_phase ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -11248,31 +11364,60 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 30 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ] ; + sh:order 33 ; + sh:path biolink:id ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:BiologicalSex ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:has_total ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -11280,6 +11425,17 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:object_specialization_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -11287,103 +11443,68 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:has_count ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:subject_direction_qualifier ], + sh:path biolink:subject_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 16 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:has_percentage ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 10 ; sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:object_aspect_qualifier ] ; + sh:order 8 ; + sh:path biolink:has_count ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . biolink:EnvironmentalExposure a sh:NodeShape ; sh:closed true ; sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -11391,151 +11512,157 @@ biolink:EnvironmentalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:EnvironmentalExposure . - -biolink:EnvironmentalFeature a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:EnvironmentalExposure . + +biolink:EnvironmentalFeature a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ] ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:EnvironmentalFeature . biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -11543,49 +11670,69 @@ biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:order 7 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:id ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; @@ -11593,54 +11740,28 @@ biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:order 2 ; sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ] ; + sh:order 14 ; + sh:path dct:description ] ; sh:targetClass biolink:EnvironmentalFoodContaminant . biolink:EnvironmentalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -11653,32 +11774,16 @@ biolink:EnvironmentalProcess a sh:NodeShape ; sh:order 8 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -11686,17 +11791,38 @@ biolink:EnvironmentalProcess a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ] ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; @@ -11726,27 +11852,45 @@ biolink:Event a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -11754,112 +11898,156 @@ biolink:Event a sh:NodeShape ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ] ; + sh:path biolink:id ] ; sh:targetClass biolink:Event . biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:closed true ; sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Transcript ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -11867,91 +12055,66 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Exon ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -11960,12 +12123,15 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -11975,258 +12141,225 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:ExonToTranscriptRelationship . + +biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between an exposure event and an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:deprecated ], + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:ExonToTranscriptRelationship . - -biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an exposure event and an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 30 ; + sh:path biolink:p_value ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:time ; - sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:order 24 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 33 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; @@ -12234,29 +12367,22 @@ biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:order 0 ; sh:path biolink:population_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ] ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ] ; sh:targetClass biolink:ExposureEventToOutcomeAssociation . biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -12264,72 +12390,46 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:original_object ], + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 36 ; + sh:path biolink:id ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 53 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -12337,126 +12437,69 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 6 ; + sh:path biolink:object_specialization_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 48 ; + sh:order 51 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; @@ -12464,50 +12507,44 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:order 48 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 46 ; + sh:order 49 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:double ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], + sh:order 50 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:class biolink:ExposureEvent ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -12519,74 +12556,184 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 40 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 47 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 29 ; sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_count ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ] ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for disease or phenotype to entity associations." ; - sh:ignoredProperties ( biolink:has_quotient biolink:sex_qualifier biolink:has_count biolink:has_total rdf:type biolink:has_percentage ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:ignoredProperties ( biolink:has_total rdf:type biolink:has_count biolink:has_percentage biolink:sex_qualifier biolink:has_quotient ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ], + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; @@ -12599,53 +12746,53 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ] ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ] ; sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . biolink:Food a sh:NodeShape ; sh:closed true ; sh:description "A substance consumed by a living organism as a source of nutrition" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; @@ -12659,31 +12806,52 @@ biolink:Food a sh:NodeShape ; sh:order 14 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -12691,61 +12859,49 @@ biolink:Food a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:is_supplement ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ] ; + sh:path biolink:category ] ; sh:targetClass biolink:Food . biolink:FoodAdditive a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -12753,72 +12909,48 @@ biolink:FoodAdditive a sh:NodeShape ; sh:order 10 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -12826,11 +12958,23 @@ biolink:FoodAdditive a sh:NodeShape ; sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 1 ; @@ -12840,13 +12984,14 @@ biolink:FoodAdditive a sh:NodeShape ; biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifier for frequency type associations" ; - sh:ignoredProperties ( biolink:object_aspect_qualifier biolink:has_percentage biolink:subject_direction_qualifier biolink:has_quotient biolink:sex_qualifier biolink:object_direction_qualifier biolink:subject_aspect_qualifier biolink:has_count biolink:qualified_predicate biolink:disease_context_qualifier rdf:type biolink:has_total ) ; - sh:property [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:ignoredProperties ( biolink:has_total biolink:anatomical_context_qualifier biolink:object_specialization_qualifier biolink:disease_context_qualifier biolink:subject_direction_qualifier rdf:type biolink:qualified_predicate biolink:subject_aspect_qualifier biolink:has_percentage biolink:has_count biolink:subject_specialization_qualifier biolink:sex_qualifier biolink:object_direction_qualifier biolink:object_aspect_qualifier biolink:has_quotient ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:frequency_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -12854,36 +12999,35 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:FrequencyQualifierMixin . biolink:FrequencyQuantifier a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:integer ; + sh:property [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:has_total ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; @@ -12902,46 +13046,63 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -12949,87 +13110,39 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -13037,59 +13150,52 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -13097,16 +13203,33 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -13114,17 +13237,38 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:FunctionalAssociation . biolink:Fungus a sh:NodeShape ; @@ -13132,55 +13276,39 @@ biolink:Fungus a sh:NodeShape ; sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -13193,22 +13321,38 @@ biolink:Fungus a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:Fungus . biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; @@ -13216,465 +13360,543 @@ biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 40 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:original_predicate ], + sh:order 35 ; + sh:path biolink:subject_closure ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 31 ; + sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 16 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path rdf:object ], + sh:order 33 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:adjusted_p_value ], + sh:order 44 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:subject_closure ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 24 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OrganismTaxon ; sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:species_context_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 46 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:timepoint ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path biolink:object_category ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_namespace ], + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 26 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:qualifier ], + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:original_subject ], + sh:order 42 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 54 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:id ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:knowledge_level ], + sh:order 21 ; + sh:path biolink:qualifiers ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:object_part_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:qualified_predicate ], + sh:order 39 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:knowledge_source ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 25 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 43 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:object_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:order 22 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 50 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 53 ; - sh:path biolink:has_attribute ], + sh:order 46 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:object_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 53 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path rdfs:label ], + sh:order 48 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 49 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:qualifiers ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 52 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:predicate ], + sh:order 11 ; + sh:path biolink:object_derivative_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 51 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 16 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:object_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:object_category ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:order 13 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:negated ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:object_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 43 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 17 ; + sh:path rdf:predicate ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:subject_label_closure ] ; sh:targetClass biolink:GeneAffectsChemicalAssociation . biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 21 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 52 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 14 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:has_percentage ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 23 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 41 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:order 22 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 18 ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 7 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 24 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 9 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:disease_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; - sh:path biolink:has_percentage ], + sh:path biolink:has_count ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_closure ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 53 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; - sh:path biolink:has_count ], + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 30 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 41 ; + sh:order 44 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -13682,172 +13904,112 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:agent_type ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:sex_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 45 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:order 42 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 8 ; + sh:path biolink:object_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; + sh:order 48 ; sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 38 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 10 ; + sh:path biolink:negated ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 47 ; + sh:order 50 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ] ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . biolink:GeneExpressionMixin a sh:NodeShape ; sh:closed false ; sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:phenotypic_state ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 2 ; + sh:path biolink:stage_qualifier ], [ sh:class biolink:AnatomicalEntity ; sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:expression_site ] ; + sh:path biolink:expression_site ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ] ; sh:targetClass biolink:GeneExpressionMixin . biolink:GeneGroupingMixin a sh:NodeShape ; @@ -13865,108 +14027,117 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 39 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:iri ], + sh:order 23 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_direction_qualifier ], + sh:order 43 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:order 27 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 24 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 31 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:order 21 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; + sh:order 53 ; sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_total ], + sh:order 41 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:order 42 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:order 16 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], + sh:order 32 ; + sh:path biolink:object_namespace ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; @@ -13974,205 +14145,209 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:id ], + sh:order 37 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_closure ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 54 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 34 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; - sh:path biolink:has_count ], + sh:path dct:description ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; + sh:order 50 ; sh:path biolink:has_percentage ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 22 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 26 ; + sh:order 29 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 48 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:iri ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:category ], + sh:order 49 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 11 ; sh:path biolink:negated ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 6 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], + sh:order 51 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 45 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; + sh:order 52 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:has_count ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ] ; + sh:order 14 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:qualifier ] ; sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:closed false ; sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -14182,30 +14357,31 @@ biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:synonym ] ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:GeneProductIsoformMixin . biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -14213,202 +14389,174 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:order 42 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 36 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], + sh:order 2 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:species_context_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:qualified_predicate ], + sh:order 38 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 35 ; + sh:path biolink:id ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; @@ -14420,554 +14568,664 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:order 23 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; - sh:path biolink:knowledge_level ] ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ] ; sh:targetClass biolink:GeneRegulatesGeneAssociation . biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( biolink:subject_form_or_variant_qualifier rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 20 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:publications ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 22 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 30 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 50 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 18 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:negated ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 34 ; + sh:order 37 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 27 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 8 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 12 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 32 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 24 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 48 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 42 ; + sh:path rdfs:label ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 16 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 45 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 36 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; + sh:order 53 ; sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 29 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 21 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 46 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:order 23 ; + sh:path biolink:original_object ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 35 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 44 ; + sh:path biolink:has_attribute ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:order 19 ; sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 38 ; + sh:path biolink:id ], [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 6 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 47 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:object_label_closure ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( biolink:subject_form_or_variant_qualifier rdf:type ) ; + sh:property [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 48 ; + sh:path biolink:has_quotient ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 4 ; + sh:order 1 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 35 ; + sh:path biolink:p_value ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 30 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . - -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( biolink:subject_form_or_variant_qualifier rdf:type ) ; - sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 9 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 52 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 3 ; + sh:path rdf:predicate ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 11 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 10 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 43 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 41 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:order 27 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 50 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 45 ; + sh:path biolink:deprecated ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 53 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 17 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path rdfs:label ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 6 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:publications ], [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 47 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 38 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 39 ; + sh:path biolink:iri ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; + sh:order 18 ; sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 15 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 21 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 25 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:category ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 34 ; + sh:order 37 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 32 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 44 ; + sh:path biolink:has_attribute ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; @@ -14975,60 +15233,18 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:subject ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 20 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:disease_context_qualifier ] ; + sh:order 16 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . biolink:GeneToEntityAssociationMixin a sh:NodeShape ; @@ -15061,93 +15277,11 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "expression relationship" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; + sh:property [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -15155,34 +15289,24 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "expression relationship" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 3 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -15190,43 +15314,35 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:order 16 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 33 ; + sh:path biolink:id ], [ sh:class biolink:AnatomicalEntity ; sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; @@ -15234,29 +15350,40 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:stage_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "can be used to indicate magnitude, or also ranking" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:quantifier_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:negated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; sh:maxCount 1 ; @@ -15264,215 +15391,146 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:GeneToExpressionSiteAssociation . - -biolink:GeneToGeneAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; - sh:ignoredProperties ( biolink:expression_site biolink:quantifier_qualifier biolink:interacting_molecules_category biolink:stage_qualifier biolink:phenotypic_state rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; + sh:order 27 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; + sh:order 26 ; sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 6 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; + sh:order 30 ; sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 14 ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:GeneToExpressionSiteAssociation . + +biolink:GeneToGeneAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; + sh:ignoredProperties ( biolink:stage_qualifier rdf:type biolink:quantifier_qualifier biolink:interacting_molecules_category biolink:phenotypic_state biolink:expression_site ) ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; @@ -15483,554 +15541,506 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:GeneToGeneAssociation . - -biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path biolink:id ], + sh:path rdfs:label ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 31 ; + sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 11 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 16 ; - sh:path biolink:agent_type ], + sh:path biolink:original_object ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; + sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; + sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:path biolink:original_predicate ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; + sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ] ; + sh:targetClass biolink:GeneToGeneAssociation . + +biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:GeneToGeneCoexpressionAssociation . - -biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 21 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 40 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "membership of the gene in the given gene family." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:path biolink:object_namespace ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; + sh:order 34 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 37 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 20 ; sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 38 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 17 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 42 ; sh:path biolink:deprecated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 24 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:stage_qualifier ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 41 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Gene ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ] ; + sh:targetClass biolink:GeneToGeneCoexpressionAssociation . + +biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Gene ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "membership of the gene in the given gene family." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:GeneToGeneFamilyAssociation . - -biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -16038,640 +16048,759 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "homology relationship type" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:GeneFamily ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:GeneToGeneHomologyAssociation . + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; + sh:targetClass biolink:GeneToGeneFamilyAssociation . -biolink:GeneToGeneProductRelationship a sh:NodeShape ; +biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A gene is transcribed and potentially translated to a gene product" ; + sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "homology relationship type" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneProductMixin ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 8 ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:GeneToGeneHomologyAssociation . + +biolink:GeneToGeneProductRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is transcribed and potentially translated to a gene product" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GeneToGeneProductRelationship . - -biolink:GeneToGoTermAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:GeneProductMixin ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:id ] ; + sh:targetClass biolink:GeneToGeneProductRelationship . + +biolink:GeneToGoTermAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; @@ -16682,507 +16811,568 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:GeneToGoTermAssociation . - -biolink:GeneToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a gene or gene product and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:GeneToGoTermAssociation . + +biolink:GeneToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a gene or gene product and a biological process or pathway." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:GeneToPathwayAssociation . biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 39 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 47 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 38 ; sh:path biolink:id ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 35 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 5 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:agent_type ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 22 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 23 ; + sh:path biolink:original_object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 50 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 31 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 18 ; - sh:path biolink:original_subject ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; + sh:order 33 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 20 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 40 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 30 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], + sh:order 49 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 11 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 25 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 6 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 29 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], + sh:order 45 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 32 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; + sh:order 53 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 44 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; @@ -17190,51 +17380,105 @@ biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 36 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 16 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 15 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ] ; + sh:order 26 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:has_count ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path dct:description ] ; sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . biolink:Genome a sh:NodeShape ; sh:closed true ; sh:description "A genome is the sum of genetic material within a cell or virion." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -17242,27 +17486,39 @@ biolink:Genome a sh:NodeShape ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -17275,65 +17531,35 @@ biolink:Genome a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:Genome . biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:closed true ; sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 8 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -17341,92 +17567,100 @@ biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:order 15 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 17 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_qualitative_value ], + sh:order 7 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:has_biological_sequence ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 8 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_gene_or_gene_product ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:synonym ] ; + sh:order 4 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; @@ -17445,70 +17679,173 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:phase ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; + sh:in ( "+" "-" "." "?" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:genome_build ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:integer ; sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:end_interbase_coordinate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:strand ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], + sh:order 41 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path rdf:predicate ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -17516,28 +17853,33 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:order 18 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 36 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:integer ; sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:start_interbase_coordinate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], [ sh:class biolink:NucleicAcidEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -17545,210 +17887,199 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], + sh:order 8 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:genome_build ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:GenomicSequenceLocalization . + +biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:GenomicSequenceLocalization . - -biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; @@ -17762,28 +18093,22 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:class biolink:Genotype ; sh:description "A genotype that has a role in modeling the disease." ; sh:maxCount 1 ; @@ -17791,100 +18116,22 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -17897,82 +18144,84 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ] ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ] ; sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:Disease ; sh:description "a disease that is associated with that genotype" ; sh:maxCount 1 ; @@ -17980,39 +18229,97 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; @@ -18020,45 +18327,25 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -18066,164 +18353,118 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 44 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ] ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ] ; sh:targetClass biolink:GenotypeToDiseaseAssociation . biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -18236,86 +18477,68 @@ biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:GenotypeToEntityAssociationMixin . biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -18324,18 +18547,39 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "the relationship type used to connect genotype to gene" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; @@ -18348,71 +18592,42 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "the relationship type used to connect genotype to gene" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Gene ; sh:description "gene implicated in genotype" ; sh:maxCount 1 ; @@ -18421,11 +18636,16 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -18433,63 +18653,71 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; + sh:order 24 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:GenotypeToGeneAssociation . biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Genotype ; sh:description "child genotype" ; sh:maxCount 1 ; @@ -18497,85 +18725,78 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -18588,17 +18809,32 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -18606,66 +18842,52 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -18673,35 +18895,47 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:GenotypeToGenotypePartAssociation . biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -18709,331 +18943,348 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 16 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 24 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 36 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:double ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 41 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:has_count ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], + sh:order 11 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 45 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], + sh:order 46 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 51 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], + sh:order 48 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 23 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 17 ; - sh:path biolink:original_predicate ], + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 49 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:path biolink:timepoint ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 29 ; + sh:order 32 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:object_specialization_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ] ; + sh:order 50 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ] ; sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; @@ -19041,153 +19292,136 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -19200,35 +19434,53 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ] ; + sh:order 3 ; + sh:path biolink:negated ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; @@ -19236,18 +19488,31 @@ biolink:GenotypicSex a sh:NodeShape ; sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -19255,44 +19520,22 @@ biolink:GenotypicSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -19300,26 +19543,35 @@ biolink:GenotypicSex a sh:NodeShape ; sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ] ; + sh:order 0 ; + sh:path rdfs:label ] ; sh:targetClass biolink:GenotypicSex . biolink:GeographicExposure a sh:NodeShape ; @@ -19327,60 +19579,27 @@ biolink:GeographicExposure a sh:NodeShape ; sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -19394,6 +19613,11 @@ biolink:GeographicExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -19401,136 +19625,156 @@ biolink:GeographicExposure a sh:NodeShape ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:GeographicExposure . biolink:GeographicLocation a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates" ; - sh:ignoredProperties ( rdf:type biolink:timepoint ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:ignoredProperties ( biolink:timepoint rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:longitude ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:float ; sh:description "latitude" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:latitude ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "longitude" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:longitude ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:GeographicLocation . biolink:GeographicLocationAtTime a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates, for a particular time" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:longitude ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -19538,211 +19782,225 @@ biolink:GeographicLocationAtTime a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:float ; + sh:description "longitude" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:longitude ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "latitude" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:latitude ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ] ; + sh:path biolink:latitude ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:GrossAnatomicalStructure . biolink:Haplotype a sh:NodeShape ; sh:closed true ; sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -19750,43 +20008,27 @@ biolink:Haplotype a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ] ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Haplotype . biolink:Hospitalization a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -19794,50 +20036,60 @@ biolink:Hospitalization a sh:NodeShape ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -19846,38 +20098,53 @@ biolink:HospitalizationOutcome a sh:NodeShape ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:HospitalizationOutcome . -biolink:Human a sh:NodeShape ; - sh:closed true ; - sh:description "A member of the the species Homo sapiens." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], +biolink:Human a sh:NodeShape ; + sh:closed true ; + sh:description "A member of the the species Homo sapiens." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -19885,49 +20152,34 @@ biolink:Human a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Human . biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; @@ -19935,24 +20187,64 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -19960,67 +20252,88 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -20028,46 +20341,56 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -20075,27 +20398,6 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -20103,60 +20405,10 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ] ; + sh:order 20 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . biolink:Invertebrate a sh:NodeShape ; @@ -20164,234 +20416,234 @@ biolink:Invertebrate a sh:NodeShape ; sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Invertebrate . biolink:JournalArticle a sh:NodeShape ; sh:closed true ; sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:order 25 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:issue ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:creation_date ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 12 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 16 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path dct:description ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:license ], + sh:order 2 ; + sh:path biolink:volume ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:keywords ], + sh:order 5 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path dct:type ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path biolink:format ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:rights ], + sh:order 14 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:category ], + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], + sh:order 7 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:format ], + sh:order 6 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:type ] ; + sh:order 18 ; + sh:path biolink:id ] ; sh:targetClass biolink:JournalArticle . biolink:LogOddsAnalysisResult a sh:NodeShape ; @@ -20399,65 +20651,76 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:description "A result of a log odds ratio analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -20465,71 +20728,53 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:order 6 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ] ; + sh:order 12 ; + sh:path rdfs:label ] ; sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -20543,33 +20788,40 @@ biolink:MacromolecularComplex a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ] ; + sh:order 2 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:MacromolecularComplex . biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; @@ -20577,256 +20829,178 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:BiologicalProcess ; - sh:description "class describing the activity, process or localization of the gene product" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . - -biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:BiologicalProcess ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -20834,46 +21008,66 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ] ; + sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . + +biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -20886,84 +21080,130 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:CellularComponent ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -20975,36 +21215,53 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:CellularComponent ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -21012,22 +21269,17 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; @@ -21042,19 +21294,19 @@ biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; @@ -21067,124 +21319,181 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -21192,98 +21501,41 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ] ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . biolink:Mammal a sh:NodeShape ; @@ -21291,59 +21543,72 @@ biolink:Mammal a sh:NodeShape ; sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -21354,20 +21619,7 @@ biolink:Mammal a sh:NodeShape ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Mammal . biolink:MappingCollection a sh:NodeShape ; @@ -21386,38 +21638,11 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -21432,66 +21657,76 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:NamedThing ; - sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -21503,22 +21738,30 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -21530,91 +21773,53 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "derivation relationship" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "derivation relationship" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ] ; - sh:targetClass biolink:MaterialSampleDerivationAssociation . - -biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a material sample and a disease or phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; @@ -21625,218 +21830,265 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:NamedThing ; + sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:iri ] ; + sh:targetClass biolink:MaterialSampleDerivationAssociation . + +biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a material sample and a disease or phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; @@ -21869,11 +22121,28 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -21881,15 +22150,33 @@ biolink:MicroRNA a sh:NodeShape ; sh:order 5 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -21897,56 +22184,21 @@ biolink:MicroRNA a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ] ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; @@ -21960,160 +22212,163 @@ biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:ModelToDiseaseAssociationMixin . biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -22132,64 +22387,61 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22197,123 +22449,103 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; + sh:order 14 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -22321,22 +22553,24 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -22344,23 +22578,77 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22368,209 +22656,176 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ] ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; @@ -22578,62 +22833,54 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22642,85 +22889,79 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:MolecularActivityToPathwayAssociation . biolink:MolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:is_toxic ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:is_supplement ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; @@ -22728,59 +22969,70 @@ biolink:MolecularMixture a sh:NodeShape ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:synonym ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -22793,129 +23045,65 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:property [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], + sh:order 2 ; + sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:iri ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:population_context_qualifier ], + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -22924,11 +23112,11 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:order 36 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -22937,153 +23125,187 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:subject_context_qualifier ], + sh:order 6 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 41 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 38 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ] ; - sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . - -biolink:NoncodingRNAProduct a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 7 ; + sh:path biolink:population_context_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 37 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:path biolink:negated ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 40 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + +biolink:NoncodingRNAProduct a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -23091,16 +23313,31 @@ biolink:NoncodingRNAProduct a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -23108,25 +23345,40 @@ biolink:NoncodingRNAProduct a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ] ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; @@ -23134,23 +23386,38 @@ biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -23162,55 +23429,40 @@ biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:NucleicAcidSequenceMotif . biolink:NucleosomeModification a sh:NodeShape ; @@ -23218,89 +23470,89 @@ biolink:NucleosomeModification a sh:NodeShape ; sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; @@ -23308,51 +23560,44 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -23360,41 +23605,48 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ] ; + sh:path biolink:id ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; @@ -23407,21 +23659,23 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:closed true ; sh:description "describes a characteristic of an organismal entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -23435,13 +23689,21 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -23452,23 +23714,8 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -23476,16 +23723,21 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:order 0 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -23498,13 +23750,13 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:closed false ; sh:description "An association between an organism taxon and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -23512,125 +23764,89 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:OrganismTaxonToEntityAssociation . biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "the environment in which the organism occurs" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "predicate describing the relationship between the taxon and the environment" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -23643,56 +23859,97 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "the environment in which the organism occurs" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -23700,109 +23957,105 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:qualifiers ] ; sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:closed false ; sh:description "A relationship between two organism taxon nodes" ; sh:ignoredProperties ( biolink:associated_environmental_context rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OrganismTaxon ; sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -23810,40 +24063,25 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -23851,200 +24089,247 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:qualifier ] ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:object_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -24052,79 +24337,90 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:order 36 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:associated_environmental_context ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -24137,214 +24433,93 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ] ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:closed true ; sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OrganismTaxon ; sh:description "the more specific taxon" ; sh:maxCount 1 ; @@ -24353,27 +24528,18 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -24385,210 +24551,234 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . - -biolink:OrganismToOrganismAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . + +biolink:OrganismToOrganismAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:IndividualOrganism ; - sh:description "An association between two individual organisms." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:IndividualOrganism ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -24596,140 +24786,156 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:IndividualOrganism ; + sh:description "An association between two individual organisms." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:OrganismToOrganismAssociation . - -biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 36 ; + sh:path dct:description ] ; + sh:targetClass biolink:OrganismToOrganismAssociation . + +biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "The relationship to the disease" ; sh:maxCount 1 ; @@ -24737,229 +24943,268 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:class biolink:OrganismalEntity ; + sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OrganismalEntity ; - sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ] ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; sh:ignoredProperties ( rdf:type biolink:interacting_molecules_category ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -24967,93 +25212,79 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "interaction relationship type" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -25061,44 +25292,69 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -25106,71 +25362,95 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ] ; + sh:path biolink:agent_type ] ; sh:targetClass biolink:PairwiseGeneToGeneInteraction . biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction at the molecular level between two physical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -25184,29 +25464,45 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -25219,24 +25515,6 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_subject ], - [ sh:class biolink:MolecularEntity ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], [ sh:class biolink:MolecularEntity ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -25244,150 +25522,124 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:MolecularEntity ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; @@ -25400,41 +25652,52 @@ biolink:Patent a sh:NodeShape ; sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 18 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 17 ; + sh:path rdf:type ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -25442,17 +25705,10 @@ biolink:Patent a sh:NodeShape ; sh:order 16 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; @@ -25461,64 +25717,60 @@ biolink:Patent a sh:NodeShape ; sh:order 14 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 19 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ] ; + sh:order 11 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -25531,34 +25783,47 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:closed true ; sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -25571,57 +25836,44 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ] ; sh:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; @@ -25635,18 +25887,6 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -25654,54 +25894,49 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -25711,7 +25946,24 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:PathologicalAnatomicalStructure . biolink:PathologicalEntityMixin a sh:NodeShape ; @@ -25724,17 +25976,17 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -25743,62 +25995,69 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:order 0 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -25806,40 +26065,33 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ] ; + sh:order 9 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:PathologicalProcess . biolink:PathologicalProcessExposure a sh:NodeShape ; sh:closed true ; sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -25847,33 +26099,46 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -25886,34 +26151,21 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:timepoint ] ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -25927,14 +26179,18 @@ biolink:Phenomenon a sh:NodeShape ; sh:description "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -25946,123 +26202,171 @@ biolink:Phenomenon a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:Phenomenon . + +biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:Phenomenon . - -biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:has_total ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:double ; + sh:order 37 ; + sh:path dct:description ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_count ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -26073,8 +26377,31 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -26082,128 +26409,85 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 42 ; + sh:path biolink:has_quotient ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 36 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 49 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -26217,460 +26501,446 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:order 43 ; sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 32 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ] ; + sh:order 9 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PhenotypicFeature ; + sh:property [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path rdf:subject ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 13 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 1 ; + sh:path biolink:has_count ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualified_predicate ], + sh:order 5 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:has_total ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:predicate ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_percentage ] ; + sh:order 9 ; + sh:path biolink:qualified_predicate ] ; sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; + sh:order 28 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], + sh:order 41 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 13 ; sh:path biolink:knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 38 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 53 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], + sh:order 49 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 32 ; + sh:order 35 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:order 8 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:double ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], + sh:order 40 ; + sh:path rdfs:label ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:has_evidence ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 20 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 46 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; - sh:path rdfs:label ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 5 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; + sh:order 42 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 50 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 6 ; + sh:path biolink:object_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 51 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 45 ; + sh:path biolink:has_total ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 43 ; + sh:path biolink:deprecated ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ] ; + sh:order 47 ; + sh:path biolink:has_percentage ] ; sh:targetClass biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . biolink:PhenotypicQuality a sh:NodeShape ; @@ -26678,126 +26948,97 @@ biolink:PhenotypicQuality a sh:NodeShape ; sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ] ; - sh:targetClass biolink:PhenotypicQuality . - -biolink:PhenotypicSex a sh:NodeShape ; - sh:closed true ; - sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:PhenotypicQuality . + +biolink:PhenotypicSex a sh:NodeShape ; + sh:closed true ; + sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -26809,40 +27050,32 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -26852,7 +27085,44 @@ biolink:PhenotypicSex a sh:NodeShape ; [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; @@ -26870,33 +27140,26 @@ biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:property [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -26905,47 +27168,60 @@ biolink:PhysiologicalProcess a sh:NodeShape ; sh:order 0 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; @@ -26956,39 +27232,52 @@ biolink:PhysiologicalProcess a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:PhysiologicalProcess . + +biolink:PlanetaryEntity a sh:NodeShape ; + sh:closed true ; + sh:description "Any entity or process that exists at the level of the whole planet" ; + sh:ignoredProperties ( biolink:longitude biolink:latitude biolink:timepoint rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ] ; - sh:targetClass biolink:PhysiologicalProcess . - -biolink:PlanetaryEntity a sh:NodeShape ; - sh:closed true ; - sh:description "Any entity or process that exists at the level of the whole planet" ; - sh:ignoredProperties ( biolink:latitude biolink:longitude rdf:type biolink:timepoint ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -26996,90 +27285,44 @@ biolink:PlanetaryEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -27088,70 +27331,83 @@ biolink:Plant a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Plant . - -biolink:Polypeptide a sh:NodeShape ; - sh:closed true ; - sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:Plant . + +biolink:Polypeptide a sh:NodeShape ; + sh:closed true ; + sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -27160,112 +27416,160 @@ biolink:Polypeptide a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Polypeptide . biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a two populations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -27277,162 +27581,128 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the object of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the subject of the association" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; + sh:order 6 ; + sh:path biolink:publications ] ; sh:targetClass biolink:PopulationToPopulationAssociation . biolink:PosttranslationalModification a sh:NodeShape ; @@ -27440,144 +27710,172 @@ biolink:PosttranslationalModification a sh:NodeShape ; sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PosttranslationalModification . biolink:PreprintPublication a sh:NodeShape ; sh:closed true ; sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:summary ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path rdfs:label ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -27585,25 +27883,25 @@ biolink:PreprintPublication a sh:NodeShape ; sh:order 12 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -27611,129 +27909,132 @@ biolink:PreprintPublication a sh:NodeShape ; sh:order 16 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:order 13 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:PreprintPublication . + +biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Describes a regulatory relationship between two genes or gene products." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 31 ; sh:path biolink:id ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ] ; - sh:targetClass biolink:PreprintPublication . - -biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Describes a regulatory relationship between two genes or gene products." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; @@ -27746,156 +28047,144 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:BiologicalProcess ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:BiologicalProcess ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:ProcessRegulatesProcessAssociation . biolink:ProcessedMaterial a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; @@ -27903,33 +28192,32 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:order 7 ; sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -27943,55 +28231,37 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ] ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ] ; sh:targetClass biolink:ProcessedMaterial . biolink:Protein a sh:NodeShape ; @@ -27999,32 +28269,21 @@ biolink:Protein a sh:NodeShape ; sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -28037,11 +28296,12 @@ biolink:Protein a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -28049,21 +28309,31 @@ biolink:Protein a sh:NodeShape ; sh:order 3 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -28071,11 +28341,11 @@ biolink:Protein a sh:NodeShape ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 5 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Protein . biolink:ProteinDomain a sh:NodeShape ; @@ -28083,83 +28353,83 @@ biolink:ProteinDomain a sh:NodeShape ; sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -28170,82 +28440,82 @@ biolink:ProteinDomain a sh:NodeShape ; biolink:ProteinFamily a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -28266,21 +28536,12 @@ biolink:ProteinIsoform a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -28292,91 +28553,91 @@ biolink:ProteinIsoform a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:ProteinIsoform . - -biolink:RNAProduct a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ProteinIsoform . + +biolink:RNAProduct a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -28389,54 +28650,64 @@ biolink:RNAProduct a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ] ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:RNAProduct . biolink:RNAProductIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -28448,46 +28719,39 @@ biolink:RNAProductIsoform a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -28503,408 +28767,282 @@ biolink:RNAProductIsoform a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:RNAProductIsoform . biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 23 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 5 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_subject ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdfs:label ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:order 39 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the chemical element that is the target of the statement" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 5 ; - sh:path rdf:object ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; sh:in ( "left" "right" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:reaction_side ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], + sh:order 34 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdf:predicate ], + sh:order 6 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], + sh:order 0 ; + sh:path biolink:stoichiometry ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 1 ; + sh:path biolink:reaction_direction ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -28912,11 +29050,27 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:order 20 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -28925,44 +29079,93 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:order 5 ; sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], + sh:order 21 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -28970,28 +29173,95 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:order 41 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 38 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path dct:description ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ] ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; @@ -28999,6 +29269,28 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -29010,6 +29302,12 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -29017,48 +29315,30 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -29067,38 +29347,28 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:order 1 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ] ; + sh:order 8 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ReagentTargetedGene . biolink:RegulatoryRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -29106,27 +29376,16 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:order 8 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -29134,49 +29393,60 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:RegulatoryRegion . biolink:RelationshipQuantifier a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( biolink:has_quotient biolink:has_count biolink:has_total rdf:type biolink:has_percentage ) ; + sh:ignoredProperties ( biolink:has_total rdf:type biolink:has_count biolink:has_percentage biolink:has_quotient ) ; sh:targetClass biolink:RelationshipQuantifier . biolink:RelationshipType a sh:NodeShape ; @@ -29197,40 +29467,6 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:description "A result of a relative frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -29245,45 +29481,79 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ] ; + sh:order 0 ; + sh:path biolink:license ] ; sh:targetClass biolink:RelativeFrequencyAnalysisResult . biolink:SensitivityQuantifier a sh:NodeShape ; @@ -29294,42 +29564,35 @@ biolink:SensitivityQuantifier a sh:NodeShape ; biolink:SequenceAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; - sh:ignoredProperties ( biolink:end_interbase_coordinate biolink:phase biolink:start_interbase_coordinate biolink:genome_build biolink:strand rdf:type ) ; + sh:ignoredProperties ( biolink:end_interbase_coordinate rdf:type biolink:phase biolink:start_interbase_coordinate biolink:strand biolink:genome_build ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -29337,40 +29600,12 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -29378,158 +29613,118 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:SequenceAssociation . - -biolink:SequenceFeatureRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "For example, a particular exon is part of a particular transcript or gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -29537,78 +29732,152 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:NucleicAcidEntity ; + [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:SequenceAssociation . + +biolink:SequenceFeatureRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "For example, a particular exon is part of a particular transcript or gene" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -29617,106 +29886,114 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:NucleicAcidEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -29724,29 +30001,22 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:original_predicate ] ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ] ; sh:targetClass biolink:SequenceFeatureRelationship . biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; @@ -29754,151 +30024,170 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:SequenceVariant ; sh:description "variant that modulates the treatment of some disease" ; sh:maxCount 1 ; @@ -29906,76 +30195,57 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ] ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . biolink:Serial a sh:NodeShape ; @@ -29983,31 +30253,44 @@ biolink:Serial a sh:NodeShape ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:rights ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:type ], + sh:order 1 ; + sh:path biolink:volume ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:summary ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:rights ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], + sh:order 0 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -30015,61 +30298,55 @@ biolink:Serial a sh:NodeShape ; sh:order 15 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:summary ], + sh:order 2 ; + sh:path biolink:issue ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; - sh:maxCount 1 ; + sh:order 22 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:keywords ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; @@ -30077,50 +30354,43 @@ biolink:Serial a sh:NodeShape ; sh:order 21 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], + sh:order 4 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:volume ], + sh:order 9 ; + sh:path dct:type ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:issue ] ; + sh:order 17 ; + sh:path biolink:id ] ; sh:targetClass biolink:Serial . biolink:SeverityValue a sh:NodeShape ; @@ -30128,243 +30398,236 @@ biolink:SeverityValue a sh:NodeShape ; sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:SeverityValue . biolink:SiRNA a sh:NodeShape ; sh:closed true ; sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; sh:closed true ; sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:is_metabolite ], - [ sh:datatype xsd:string ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; @@ -30372,17 +30635,27 @@ biolink:SmallMolecule a sh:NodeShape ; sh:order 1 ; sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -30390,18 +30663,15 @@ biolink:SmallMolecule a sh:NodeShape ; sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:order 14 ; + sh:path rdfs:label ] ; sh:targetClass biolink:SmallMolecule . biolink:Snv a sh:NodeShape ; @@ -30409,22 +30679,27 @@ biolink:Snv a sh:NodeShape ; sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The state of the sequence w.r.t a reference sequence" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:has_gene ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30432,40 +30707,38 @@ biolink:Snv a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -30473,53 +30746,45 @@ biolink:Snv a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ] ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ] ; sh:targetClass biolink:Snv . biolink:SocioeconomicExposure a sh:NodeShape ; sh:closed true ; sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:SocioeconomicAttribute ; + sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -30527,39 +30792,63 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -30570,31 +30859,12 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:SocioeconomicAttribute ; - sh:description "connects any entity to an attribute" ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ] ; + sh:order 9 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:SocioeconomicExposure . biolink:SocioeconomicOutcome a sh:NodeShape ; @@ -30613,11 +30883,15 @@ biolink:StudyPopulation a sh:NodeShape ; sh:description "A group of people banded together or treated as a group as participants in a research study." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -30629,17 +30903,6 @@ biolink:StudyPopulation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30647,15 +30910,22 @@ biolink:StudyPopulation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -30667,29 +30937,29 @@ biolink:StudyPopulation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:StudyPopulation . biolink:StudyResult a sh:NodeShape ; @@ -30697,69 +30967,52 @@ biolink:StudyResult a sh:NodeShape ; sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -30773,17 +31026,34 @@ biolink:StudyResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ] ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:StudyResult . biolink:StudyVariable a sh:NodeShape ; @@ -30791,93 +31061,93 @@ biolink:StudyVariable a sh:NodeShape ; sh:description "a variable that is used as a measure in the investigation of a study" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ] ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; @@ -30889,91 +31159,62 @@ biolink:SubjectOfInvestigation a sh:NodeShape ; biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30981,97 +31222,149 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -31084,50 +31377,27 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; + sh:order 33 ; + sh:path biolink:category ] ; sh:targetClass biolink:TaxonToTaxonAssociation . biolink:TextMiningResult a sh:NodeShape ; sh:closed true ; sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -31135,36 +31405,39 @@ biolink:TextMiningResult a sh:NodeShape ; sh:order 13 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -31172,40 +31445,37 @@ biolink:TextMiningResult a sh:NodeShape ; sh:order 12 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ] ; + sh:order 4 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:TextMiningResult . biolink:ThingWithTaxon a sh:NodeShape ; @@ -31230,87 +31500,50 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:description "A gene is a collection of transcripts" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -31318,47 +31551,39 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -31366,23 +31591,42 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Transcript ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -31391,97 +31635,116 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ] ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ] ; sh:targetClass biolink:TranscriptToGeneRelationship . biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -31489,11 +31752,14 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:order 9 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -31505,87 +31771,196 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:TranscriptionFactorBindingSite . biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -31593,68 +31968,55 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -31662,136 +32024,44 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -31799,102 +32069,102 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ] ; + sh:order 32 ; + sh:path biolink:iri ] ; sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; + sh:property [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -31902,66 +32172,67 @@ biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 44 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; @@ -31969,103 +32240,102 @@ biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:order 43 ; sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "E.g. is pathogenic for" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ] ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:VariantToDiseaseAssociation . biolink:VariantToEntityAssociationMixin a sh:NodeShape ; @@ -32097,159 +32367,124 @@ biolink:VariantToEntityAssociationMixin a sh:NodeShape ; biolink:VariantToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; - sh:ignoredProperties ( biolink:expression_site biolink:quantifier_qualifier biolink:stage_qualifier biolink:phenotypic_state rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:ignoredProperties ( biolink:stage_qualifier rdf:type biolink:quantifier_qualifier biolink:phenotypic_state biolink:expression_site ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; @@ -32257,159 +32492,149 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ] ; - sh:targetClass biolink:VariantToGeneAssociation . - -biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 8 ; sh:path biolink:knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 7 ; + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:VariantToGeneAssociation . + +biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 34 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 39 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -32421,55 +32646,70 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 3 ; + sh:path biolink:phenotypic_state ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 36 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; @@ -32479,36 +32719,64 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], + sh:order 2 ; + sh:path biolink:stage_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -32516,92 +32784,127 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:path biolink:subject_namespace ] ; + sh:targetClass biolink:VariantToGeneExpressionAssociation . + +biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 8 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 30 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 44 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:VariantToGeneExpressionAssociation . - -biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:BiologicalSex ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; sh:maxCount 1 ; @@ -32609,326 +32912,367 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 49 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 24 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 21 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 48 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; + sh:order 31 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; - sh:path biolink:has_count ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:path dct:description ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 52 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 9 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], + sh:order 40 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 36 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; + sh:order 53 ; sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 27 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; + sh:order 42 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 39 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 47 ; + sh:path biolink:has_percentage ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 26 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 45 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:disease_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:object_specialization_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 48 ; + sh:order 51 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 19 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 50 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:object_category ] ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:property [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdf:type ], + sh:order 40 ; + sh:path rdfs:label ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], + sh:order 36 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:integer ; + sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_count ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 19 ; + sh:path biolink:original_subject ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; @@ -32936,94 +33280,83 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:integer ; sh:description "number all populations that carry a particular allele, aka allele number" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], + sh:order 41 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -33031,105 +33364,60 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:order 37 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:double ; - sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:has_quotient ], + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:double ; + sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:order 39 ; + sh:path rdf:type ] ; sh:targetClass biolink:VariantToPopulationAssociation . biolink:Vertebrate a sh:NodeShape ; @@ -33137,54 +33425,61 @@ biolink:Vertebrate a sh:NodeShape ; sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -33197,23 +33492,16 @@ biolink:Vertebrate a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ] ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Vertebrate . biolink:Virus a sh:NodeShape ; @@ -33221,38 +33509,20 @@ biolink:Virus a sh:NodeShape ; sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -33261,103 +33531,68 @@ biolink:Virus a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:Virus . - -biolink:WebPage a sh:NodeShape ; - sh:closed true ; - sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 13 ; sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:Virus . + +biolink:WebPage a sh:NodeShape ; + sh:closed true ; + sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -33368,6 +33603,17 @@ biolink:WebPage a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -33380,38 +33626,68 @@ biolink:WebPage a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; @@ -33420,149 +33696,153 @@ biolink:WebPage a sh:NodeShape ; sh:order 14 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ] ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:WebPage . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ] ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Behavior . biolink:BehavioralFeature a sh:NodeShape ; sh:closed true ; sh:description "A phenotypic feature which is behavioral in nature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -33580,55 +33860,62 @@ biolink:BehavioralFeature a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:BehavioralFeature . biolink:CellularComponent a sh:NodeShape ; sh:closed true ; sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -33642,42 +33929,38 @@ biolink:CellularComponent a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -33685,40 +33968,23 @@ biolink:CellularComponent a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:CellularComponent . biolink:ClinicalAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; @@ -33729,6 +33995,12 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -33739,12 +34011,18 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -33752,11 +34030,21 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -33770,17 +34058,17 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ClinicalAttribute . biolink:Dataset a sh:NodeShape ; @@ -33788,219 +34076,208 @@ biolink:Dataset a sh:NodeShape ; sh:description "an item that refers to a collection of data from a data source." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Dataset . biolink:DatasetDistribution a sh:NodeShape ; sh:closed true ; sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:format ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:distribution_download_url ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:creation_date ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:license ], + sh:order 2 ; + sh:path biolink:rights ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:distribution_download_url ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ] ; + sh:order 12 ; + sh:path rdf:type ] ; sh:targetClass biolink:DatasetDistribution . biolink:Device a sh:NodeShape ; sh:closed true ; sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -34008,22 +34285,23 @@ biolink:Device a sh:NodeShape ; sh:order 9 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34032,68 +34310,64 @@ biolink:Device a sh:NodeShape ; sh:order 4 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Device . biolink:Exon a sh:NodeShape ; sh:closed true ; sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -34101,17 +34375,9 @@ biolink:Exon a sh:NodeShape ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34120,35 +34386,46 @@ biolink:Exon a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Exon . biolink:GeneFamily a sh:NodeShape ; sh:closed true ; sh:description "any grouping of multiple genes or gene products related by common descent" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], @@ -34158,18 +34435,6 @@ biolink:GeneFamily a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -34177,42 +34442,65 @@ biolink:GeneFamily a sh:NodeShape ; sh:order 9 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34231,39 +34519,35 @@ biolink:GeneProductMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeneProductMixin . biolink:GeneticInheritance a sh:NodeShape ; sh:closed true ; sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -34271,21 +34555,11 @@ biolink:GeneticInheritance a sh:NodeShape ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -34299,63 +34573,80 @@ biolink:GeneticInheritance a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:GeneticInheritance . biolink:InformationContentEntity a sh:NodeShape ; sh:closed false ; sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; - sh:ignoredProperties ( biolink:published_in biolink:upstream_resource_ids biolink:authors biolink:mesh_terms schema1:logo biolink:issue dct:distribution biolink:resource_id biolink:source_web_page biolink:chapter biolink:has_dataset biolink:resource_role biolink:volume biolink:summary biolink:pages biolink:ingest_date biolink:keywords biolink:iso_abbreviation biolink:distribution_download_url dct:type rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:ignoredProperties ( biolink:chapter rdf:type biolink:issue biolink:authors biolink:upstream_resource_ids dct:distribution dct:type biolink:published_in schema1:logo biolink:pages biolink:summary biolink:resource_id biolink:keywords biolink:has_dataset biolink:volume biolink:resource_role biolink:distribution_download_url biolink:iso_abbreviation biolink:source_web_page biolink:mesh_terms biolink:ingest_date ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34364,62 +34655,59 @@ biolink:InformationContentEntity a sh:NodeShape ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:InformationContentEntity . biolink:Onset a sh:NodeShape ; @@ -34431,11 +34719,23 @@ biolink:Onset a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -34448,6 +34748,11 @@ biolink:Onset a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34455,84 +34760,75 @@ biolink:Onset a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Onset . biolink:OrganismalEntity a sh:NodeShape ; sh:closed false ; sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -34540,16 +34836,29 @@ biolink:OrganismalEntity a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34557,6 +34866,11 @@ biolink:OrganismalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -34564,37 +34878,11 @@ biolink:OrganismalEntity a sh:NodeShape ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:OrganismalEntity . biolink:PredicateMapping a sh:NodeShape ; @@ -34602,50 +34890,44 @@ biolink:PredicateMapping a sh:NodeShape ; sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:NamedThing ; - sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:exact_match ], - [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:subject_part_qualifier ], + sh:order 20 ; + sh:path biolink:broad_match ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:subject_derivative_qualifier ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 19 ; + sh:path biolink:narrow_match ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; @@ -34653,62 +34935,62 @@ biolink:PredicateMapping a sh:NodeShape ; sh:order 1 ; sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], + sh:order 4 ; + sh:path biolink:subject_part_qualifier ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:object_derivative_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:causal_mechanism_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_qualifier ], + sh:order 14 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ], + sh:order 8 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:object_context_qualifier ], + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:exact_match ], + [ sh:datatype xsd:string ; + sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:mapped_predicate ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; @@ -34719,7 +35001,13 @@ biolink:PredicateMapping a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:object_part_qualifier ] ; + sh:path biolink:object_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; @@ -34727,16 +35015,10 @@ biolink:Procedure a sh:NodeShape ; sh:description "A series of actions conducted in a certain order or manner" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34744,80 +35026,72 @@ biolink:Procedure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Procedure . biolink:SocioeconomicAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a socioeconomic manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34825,28 +35099,33 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -34854,36 +35133,45 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:order 0 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:synonym ] ; + sh:path biolink:synonym ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:TaxonomicRank a sh:NodeShape ; @@ -34903,55 +35191,21 @@ biolink:Treatment a sh:NodeShape ; sh:closed true ; sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -34965,78 +35219,128 @@ biolink:Treatment a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], - [ sh:class biolink:Drug ; - sh:description "connects an entity to one or more drugs" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_drug ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:Device ; sh:description "connects an entity to one or more (medical) devices" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_device ], + [ sh:class biolink:Drug ; + sh:description "connects an entity to one or more drugs" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_drug ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Treatment . biolink:Zygosity a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -35050,115 +35354,99 @@ biolink:Zygosity a sh:NodeShape ; sh:order 6 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:Zygosity . biolink:Case a sh:NodeShape ; sh:closed true ; sh:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -35170,12 +35458,12 @@ biolink:Case a sh:NodeShape ; biolink:CellLine a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; @@ -35186,29 +35474,32 @@ biolink:CellLine a sh:NodeShape ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -35216,26 +35507,23 @@ biolink:CellLine a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -35243,11 +35531,11 @@ biolink:CellLine a sh:NodeShape ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:CellLine . biolink:IndividualOrganism a sh:NodeShape ; @@ -35261,28 +35549,40 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -35294,44 +35594,32 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ] ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:IndividualOrganism . biolink:Outcome a sh:NodeShape ; @@ -35345,17 +35633,33 @@ biolink:Transcript a sh:NodeShape ; sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -35363,119 +35667,84 @@ biolink:Transcript a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:order 2 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Transcript . biolink:BiologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -35483,72 +35752,95 @@ biolink:BiologicalProcess a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ] ; + sh:order 14 ; + sh:path dct:description ] ; sh:targetClass biolink:BiologicalProcess . biolink:Drug a sh:NodeShape ; sh:closed true ; sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:is_toxic ], + sh:order 11 ; + sh:path biolink:xref ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 6 ; sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "" ; + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:is_supplement ], + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -35559,107 +35851,103 @@ biolink:Drug a sh:NodeShape ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 4 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:iri ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:trade_name ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:drug_regulatory_status_world_wide ] ; sh:targetClass biolink:Drug . biolink:ExposureEvent a sh:NodeShape ; sh:closed false ; sh:description "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:id ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ] ; + sh:path biolink:id ] ; sh:targetClass biolink:ExposureEvent . biolink:MaterialSample a sh:NodeShape ; @@ -35673,16 +35961,6 @@ biolink:MaterialSample a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -35694,6 +35972,10 @@ biolink:MaterialSample a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -35707,9 +35989,10 @@ biolink:MaterialSample a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -35723,65 +36006,98 @@ biolink:MaterialSample a sh:NodeShape ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ] ; sh:targetClass biolink:MaterialSample . biolink:Pathway a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -35792,45 +36108,17 @@ biolink:Pathway a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ] ; + sh:order 1 ; + sh:path biolink:has_input ] ; sh:targetClass biolink:Pathway . biolink:LifeStage a sh:NodeShape ; @@ -35838,16 +36126,11 @@ biolink:LifeStage a sh:NodeShape ; sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -35855,166 +36138,176 @@ biolink:LifeStage a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:LifeStage . biolink:NucleicAcidEntity a sh:NodeShape ; sh:closed true ; sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:is_metabolite ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_metabolite ], + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; @@ -36022,22 +36315,17 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:order 8 ; sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ] ; + sh:order 17 ; + sh:path rdfs:label ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:MolecularActivity a sh:NodeShape ; @@ -36045,26 +36333,12 @@ biolink:MolecularActivity a sh:NodeShape ; sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -36076,43 +36350,51 @@ biolink:MolecularActivity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the output for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "The gene product, gene, or complex that catalyzes the reaction" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:enabled_by ], + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the input for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the output for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -36120,44 +36402,63 @@ biolink:MolecularActivity a sh:NodeShape ; sh:order 13 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the input for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ] ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ] ; sh:targetClass biolink:MolecularActivity . biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:closed true ; sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -36170,33 +36471,20 @@ biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -36204,29 +36492,29 @@ biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . biolink:MacromolecularMachineMixin a sh:NodeShape ; sh:closed false ; sh:description "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; - sh:ignoredProperties ( biolink:synonym rdf:type biolink:xref ) ; + sh:ignoredProperties ( biolink:synonym biolink:xref rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -36238,16 +36526,13 @@ biolink:MacromolecularMachineMixin a sh:NodeShape ; biolink:MolecularEntity a sh:NodeShape ; sh:closed true ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; - sh:ignoredProperties ( biolink:has_biological_sequence biolink:in_taxon_label rdf:type biolink:in_taxon ) ; - sh:property [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; + sh:ignoredProperties ( biolink:in_taxon biolink:in_taxon_label biolink:has_biological_sequence rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36255,21 +36540,27 @@ biolink:MolecularEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:id ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; @@ -36277,68 +36568,65 @@ biolink:MolecularEntity a sh:NodeShape ; sh:order 0 ; sh:path biolink:is_metabolite ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:trade_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:iri ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:MolecularEntity . biolink:PhysicalEntity a sh:NodeShape ; @@ -36346,26 +36634,16 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:description "An entity that has material reality (a.k.a. physical essence)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -36373,27 +36651,26 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:order 5 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -36401,17 +36678,28 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ] ; sh:targetClass biolink:PhysicalEntity . biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; @@ -36425,164 +36713,162 @@ biolink:Genotype a sh:NodeShape ; sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:Zygosity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Zygosity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:Genotype . - -biolink:SequenceVariant a sh:NodeShape ; - sh:closed true ; - sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:path biolink:xref ] ; + sh:targetClass biolink:Genotype . + +biolink:SequenceVariant a sh:NodeShape ; + sh:closed true ; + sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -36590,63 +36876,53 @@ biolink:SequenceVariant a sh:NodeShape ; sh:order 7 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], + sh:order 12 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:order 5 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:SequenceVariant . biolink:ChemicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; - sh:ignoredProperties ( biolink:is_metabolite biolink:in_taxon biolink:has_biological_sequence biolink:in_taxon_label biolink:highest_FDA_approval_status biolink:drug_regulatory_status_world_wide biolink:is_supplement biolink:routes_of_delivery rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:ignoredProperties ( rdf:type biolink:is_metabolite biolink:highest_FDA_approval_status biolink:in_taxon_label biolink:has_biological_sequence biolink:in_taxon biolink:drug_regulatory_status_world_wide biolink:routes_of_delivery biolink:is_supplement ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -36658,28 +36934,17 @@ biolink:ChemicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36687,27 +36952,50 @@ biolink:ChemicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:synonym ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ] ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ] ; sh:targetClass biolink:ChemicalEntity . biolink:Agent a sh:NodeShape ; @@ -36719,6 +37007,28 @@ biolink:Agent a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; sh:maxCount 1 ; @@ -36726,72 +37036,50 @@ biolink:Agent a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:affiliation ], + [ sh:datatype xsd:string ; + sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:address ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:address ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ] ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Agent . biolink:PhenotypicFeature a sh:NodeShape ; @@ -36799,24 +37087,6 @@ biolink:PhenotypicFeature a sh:NodeShape ; sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; @@ -36828,37 +37098,54 @@ biolink:PhenotypicFeature a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -36866,29 +37153,51 @@ biolink:PhenotypicFeature a sh:NodeShape ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:PhenotypicFeature . biolink:ChemicalRole a sh:NodeShape ; sh:closed true ; sh:description "A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -36900,18 +37209,6 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -36929,16 +37226,6 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -36946,22 +37233,23 @@ biolink:ChemicalRole a sh:NodeShape ; sh:order 3 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; @@ -36973,161 +37261,167 @@ biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ] ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeature . biolink:Gene a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Symbol for a particular thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:symbol ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37135,18 +37429,12 @@ biolink:Gene a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ] ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Gene . biolink:BiologicalSex a sh:NodeShape ; @@ -37159,25 +37447,17 @@ biolink:BiologicalSex a sh:NodeShape ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -37190,22 +37470,38 @@ biolink:BiologicalSex a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -37213,30 +37509,22 @@ biolink:BiologicalSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:BiologicalSex . biolink:AnatomicalEntity a sh:NodeShape ; @@ -37251,31 +37539,16 @@ biolink:AnatomicalEntity a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -37287,46 +37560,61 @@ biolink:AnatomicalEntity a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:AnatomicalEntity . biolink:GeneOrGeneProduct a sh:NodeShape ; sh:closed false ; sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; - sh:ignoredProperties ( biolink:synonym rdf:type biolink:xref ) ; + sh:ignoredProperties ( biolink:synonym biolink:xref rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -37357,55 +37645,45 @@ biolink:Disease a sh:NodeShape ; sh:closed true ; sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -37413,10 +37691,10 @@ biolink:Disease a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37424,139 +37702,160 @@ biolink:Disease a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:Disease . biolink:OrganismTaxon a sh:NodeShape ; sh:closed true ; sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:synonym ], - [ sh:class biolink:TaxonomicRank ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_taxonomic_rank ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:deprecated ], + [ sh:class biolink:TaxonomicRank ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_taxonomic_rank ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdf:type ] ; sh:targetClass biolink:OrganismTaxon . biolink:NamedThing a sh:NodeShape ; sh:closed true ; sh:description "a databased entity or concept/class" ; - sh:ignoredProperties ( biolink:creation_date biolink:upstream_resource_ids biolink:authors biolink:trade_name biolink:format biolink:has_output biolink:routes_of_delivery biolink:mesh_terms schema1:logo biolink:has_quantitative_value biolink:issue dct:distribution biolink:has_biological_sequence biolink:in_taxon_label biolink:license biolink:available_from biolink:timepoint biolink:summary biolink:pages biolink:ingest_date biolink:is_metabolite biolink:has_drug biolink:has_gene biolink:symbol biolink:has_procedure biolink:iso_abbreviation biolink:longitude dct:type rdf:type biolink:published_in biolink:has_chemical_role biolink:rights biolink:highest_FDA_approval_status biolink:has_attribute_type biolink:latitude biolink:in_taxon biolink:max_tolerated_dose biolink:has_qualitative_value biolink:is_supplement biolink:resource_id biolink:affiliation biolink:source_web_page biolink:enabled_by biolink:chapter biolink:has_gene_or_gene_product biolink:has_dataset biolink:address biolink:drug_regulatory_status_world_wide biolink:resource_role biolink:volume biolink:has_input biolink:keywords biolink:has_taxonomic_rank biolink:has_device biolink:is_toxic biolink:has_zygosity biolink:distribution_download_url ) ; + sh:ignoredProperties ( biolink:has_chemical_role biolink:chapter biolink:has_device biolink:timepoint dct:distribution biolink:upstream_resource_ids biolink:routes_of_delivery dct:type biolink:trade_name biolink:format biolink:enabled_by biolink:has_biological_sequence schema1:logo biolink:pages biolink:summary biolink:max_tolerated_dose biolink:resource_id biolink:keywords biolink:volume biolink:is_supplement biolink:creation_date biolink:available_from biolink:has_procedure biolink:has_gene biolink:symbol biolink:affiliation biolink:rights rdf:type biolink:issue biolink:address biolink:has_attribute_type biolink:authors biolink:has_output biolink:has_qualitative_value biolink:has_quantitative_value biolink:is_metabolite biolink:published_in biolink:longitude biolink:has_input biolink:license biolink:latitude biolink:has_zygosity biolink:has_gene_or_gene_product biolink:has_taxonomic_rank biolink:has_dataset biolink:in_taxon biolink:resource_role biolink:distribution_download_url biolink:is_toxic biolink:iso_abbreviation biolink:highest_FDA_approval_status biolink:in_taxon_label biolink:source_web_page biolink:has_drug biolink:drug_regulatory_status_world_wide biolink:mesh_terms biolink:ingest_date ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -37564,154 +37863,164 @@ biolink:NamedThing a sh:NodeShape ; sh:order 5 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ] ; + sh:order 0 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:NamedThing . biolink:EvidenceType a sh:NodeShape ; sh:closed true ; sh:description "Class of evidence that supports an association" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ] ; + sh:order 9 ; + sh:path biolink:iri ] ; sh:targetClass biolink:EvidenceType . biolink:Publication a sh:NodeShape ; sh:closed true ; sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; - sh:ignoredProperties ( biolink:published_in biolink:issue biolink:chapter biolink:iso_abbreviation biolink:volume rdf:type ) ; + sh:ignoredProperties ( biolink:chapter rdf:type biolink:issue biolink:iso_abbreviation biolink:published_in biolink:volume ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; @@ -37719,44 +38028,33 @@ biolink:Publication a sh:NodeShape ; sh:order 18 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; @@ -37764,92 +38062,104 @@ biolink:Publication a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ] ; + sh:path rdf:type ] ; sh:targetClass biolink:Publication . biolink:RetrievalSource a sh:NodeShape ; sh:closed true ; sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:deprecated ], + sh:order 15 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 18 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:order 5 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:upstream_resource_ids ], + sh:order 12 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; @@ -37857,96 +38167,75 @@ biolink:RetrievalSource a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:resource_id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:upstream_resource_ids ], [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:resource_role ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:creation_date ], + sh:order 11 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:rights ] ; + sh:order 10 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:RetrievalSource . biolink:Study a sh:NodeShape ; sh:closed true ; sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -37954,87 +38243,107 @@ biolink:Study a sh:NodeShape ; sh:order 8 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:Study . biolink:Attribute a sh:NodeShape ; sh:closed true ; sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; - sh:ignoredProperties ( biolink:in_taxon biolink:has_biological_sequence biolink:in_taxon_label biolink:has_gene_or_gene_product biolink:timepoint rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:ignoredProperties ( rdf:type biolink:has_gene_or_gene_product biolink:in_taxon_label biolink:has_biological_sequence biolink:timepoint biolink:in_taxon ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -38047,48 +38356,27 @@ biolink:Attribute a sh:NodeShape ; sh:order 2 ; sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; sh:closed false ; sh:description "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; - sh:ignoredProperties ( rdf:type biolink:timepoint ) ; + sh:ignoredProperties ( biolink:timepoint rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; diff --git a/project/shex/biolink_model.shex b/project/shex/biolink_model.shex index b166f11c1..6129d083d 100644 --- a/project/shex/biolink_model.shex +++ b/project/shex/biolink_model.shex @@ -336,6 +336,9 @@ linkml:Sparqlpath xsd:string @linkml:String ? ; @ ? ; @ ? ; + @linkml:Uriorcurie ? ; + @linkml:Uriorcurie ? ; + @linkml:String ? ; @linkml:Integer ? ; @linkml:Integer ? ; @linkml:Double ? ; @@ -503,6 +506,9 @@ linkml:Sparqlpath xsd:string @linkml:String ? ; @ ? ; @ ? ; + @linkml:Uriorcurie ? ; + @linkml:Uriorcurie ? ; + @linkml:String ? ; @linkml:Integer ? ; @linkml:Integer ? ; @linkml:Double ? ; @@ -1427,7 +1433,10 @@ linkml:Sparqlpath xsd:string ] ? ; @linkml:String ? ; @ ? ; - @ ? + @ ? ; + @linkml:Uriorcurie ? ; + @linkml:Uriorcurie ? ; + @linkml:String ? ) ; rdf:type [ ] ) @@ -1640,6 +1649,9 @@ linkml:Sparqlpath xsd:string rdf:object @ ; @ ? ; @ ? ; + @linkml:Uriorcurie ? ; + @linkml:Uriorcurie ? ; + @linkml:String ? ; @linkml:Integer ? ; @linkml:Integer ? ; @linkml:Double ? ; @@ -1777,6 +1789,9 @@ linkml:Sparqlpath xsd:string @linkml:String ? ; @ ? ; @ ? ; + @linkml:Uriorcurie ? ; + @linkml:Uriorcurie ? ; + @linkml:String ? ; @linkml:Integer ? ; @linkml:Integer ? ; @linkml:Double ? ; @@ -2326,6 +2341,9 @@ linkml:Sparqlpath xsd:string @linkml:String ? ; @ ? ; @ ? ; + @linkml:Uriorcurie ? ; + @linkml:Uriorcurie ? ; + @linkml:String ? ; @linkml:Integer ? ; @linkml:Integer ? ; @linkml:Double ? ; @@ -2641,6 +2659,9 @@ linkml:Sparqlpath xsd:string @linkml:String ? ; @ ? ; @ ? ; + @linkml:Uriorcurie ? ; + @linkml:Uriorcurie ? ; + @linkml:String ? ; @linkml:Integer ? ; @linkml:Integer ? ; @linkml:Double ? ; @@ -3492,7 +3513,10 @@ linkml:Sparqlpath xsd:string @linkml:Integer ? ; @linkml:Double ? ; @linkml:Double ? ; - @ ? + @ ? ; + @linkml:Uriorcurie ? ; + @linkml:Uriorcurie ? ; + @linkml:String ? ) ; rdf:type [ ] ) @@ -4276,6 +4300,9 @@ linkml:Sparqlpath xsd:string @linkml:String ? ; @ ? ; @ ? ; + @linkml:Uriorcurie ? ; + @linkml:Uriorcurie ? ; + @linkml:String ? ; @linkml:Integer ? ; @linkml:Integer ? ; @linkml:Double ? ; diff --git a/src/biolink_model/datamodel/model.py b/src/biolink_model/datamodel/model.py index ba2e0e7b0..062222cdb 100644 --- a/src/biolink_model/datamodel/model.py +++ b/src/biolink_model/datamodel/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-11-07T15:54:44 +# Generation date: 2024-11-07T16:11:40 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -8499,7 +8499,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(Association): """ This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic - feature where the disesae or phenotypic feature is a secondary undesirable effect. + feature where the disease or phenotypic feature is a secondary undesirable effect. """ _inherited_slots: ClassVar[List[str]] = [] @@ -9714,6 +9714,9 @@ class EntityToPhenotypicFeatureAssociationMixin(EntityToFeatureOrDiseaseQualifie object: Union[str, PhenotypicFeatureId] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None has_count: Optional[int] = None has_total: Optional[int] = None has_quotient: Optional[float] = None @@ -9741,6 +9744,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + if self.has_count is not None and not isinstance(self.has_count, int): self.has_count = int(self.has_count) @@ -9825,6 +9837,9 @@ class PhenotypicFeatureToPhenotypicFeatureAssociation(Association): qualified_predicate: Optional[str] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9871,6 +9886,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + super().__post_init__(**kwargs) if not isinstance(self.category, list): self.category = [self.category] if self.category is not None else [] @@ -10169,6 +10193,9 @@ class GenotypeToPhenotypicFeatureAssociation(Association): qualified_predicate: Optional[str] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10215,6 +10242,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + super().__post_init__(**kwargs) if not isinstance(self.category, list): self.category = [self.category] if self.category is not None else [] @@ -10248,6 +10284,9 @@ class ExposureEventToPhenotypicFeatureAssociation(Association): qualified_predicate: Optional[str] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10294,6 +10333,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + super().__post_init__(**kwargs) if not isinstance(self.category, list): self.category = [self.category] if self.category is not None else [] @@ -10332,6 +10380,9 @@ class DiseaseToPhenotypicFeatureAssociation(Association): qualified_predicate: Optional[str] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10393,6 +10444,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + super().__post_init__(**kwargs) if not isinstance(self.category, list): self.category = [self.category] if self.category is not None else [] @@ -10426,6 +10486,9 @@ class CaseToPhenotypicFeatureAssociation(Association): qualified_predicate: Optional[str] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10472,6 +10535,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + super().__post_init__(**kwargs) if not isinstance(self.category, list): self.category = [self.category] if self.category is not None else [] @@ -10505,6 +10577,9 @@ class BehaviorToBehavioralFeatureAssociation(Association): qualified_predicate: Optional[str] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10551,6 +10626,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + super().__post_init__(**kwargs) if not isinstance(self.category, list): self.category = [self.category] if self.category is not None else [] @@ -10644,6 +10728,9 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(Association): qualified_predicate: Optional[str] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10690,6 +10777,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + super().__post_init__(**kwargs) if not isinstance(self.category, list): self.category = [self.category] if self.category is not None else [] @@ -10717,6 +10813,9 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia qualified_predicate: Optional[str] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10752,6 +10851,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + super().__post_init__(**kwargs) if not isinstance(self.category, list): self.category = [self.category] if self.category is not None else [] @@ -11284,6 +11392,9 @@ class VariantToPhenotypicFeatureAssociation(Association): qualified_predicate: Optional[str] = None sex_qualifier: Optional[Union[str, BiologicalSexId]] = None disease_context_qualifier: Optional[Union[str, DiseaseId]] = None + subject_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + object_specialization_qualifier: Optional[Union[str, URIorCURIE]] = None + anatomical_context_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11330,6 +11441,15 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.disease_context_qualifier is not None and not isinstance(self.disease_context_qualifier, DiseaseId): self.disease_context_qualifier = DiseaseId(self.disease_context_qualifier) + if self.subject_specialization_qualifier is not None and not isinstance(self.subject_specialization_qualifier, URIorCURIE): + self.subject_specialization_qualifier = URIorCURIE(self.subject_specialization_qualifier) + + if self.object_specialization_qualifier is not None and not isinstance(self.object_specialization_qualifier, URIorCURIE): + self.object_specialization_qualifier = URIorCURIE(self.object_specialization_qualifier) + + if self.anatomical_context_qualifier is not None and not isinstance(self.anatomical_context_qualifier, str): + self.anatomical_context_qualifier = str(self.anatomical_context_qualifier) + super().__post_init__(**kwargs) if not isinstance(self.category, list): self.category = [self.category] if self.category is not None else [] @@ -13925,7 +14045,7 @@ class slots: model_uri=BIOLINK.subject_aspect_qualifier, domain=Association, range=Optional[str]) slots.subject_specialization_qualifier = Slot(uri=BIOLINK.subject_specialization_qualifier, name="subject specialization qualifier", curie=BIOLINK.curie('subject_specialization_qualifier'), - model_uri=BIOLINK.subject_specialization_qualifier, domain=None, range=Optional[str]) + model_uri=BIOLINK.subject_specialization_qualifier, domain=Association, range=Optional[Union[str, URIorCURIE]]) slots.subject_form_or_variant_qualifier = Slot(uri=BIOLINK.subject_form_or_variant_qualifier, name="subject form or variant qualifier", curie=BIOLINK.curie('subject_form_or_variant_qualifier'), model_uri=BIOLINK.subject_form_or_variant_qualifier, domain=Association, range=Optional[str]) @@ -13945,6 +14065,9 @@ class slots: slots.object_aspect_qualifier = Slot(uri=BIOLINK.object_aspect_qualifier, name="object aspect qualifier", curie=BIOLINK.curie('object_aspect_qualifier'), model_uri=BIOLINK.object_aspect_qualifier, domain=Association, range=Optional[str]) +slots.object_specialization_qualifier = Slot(uri=BIOLINK.object_specialization_qualifier, name="object specialization qualifier", curie=BIOLINK.curie('object_specialization_qualifier'), + model_uri=BIOLINK.object_specialization_qualifier, domain=Association, range=Optional[Union[str, URIorCURIE]]) + slots.object_form_or_variant_qualifier = Slot(uri=BIOLINK.object_form_or_variant_qualifier, name="object form or variant qualifier", curie=BIOLINK.curie('object_form_or_variant_qualifier'), model_uri=BIOLINK.object_form_or_variant_qualifier, domain=Association, range=Optional[str]) diff --git a/src/biolink_model/datamodel/pydanticmodel_v2.py b/src/biolink_model/datamodel/pydanticmodel_v2.py index a01154093..472c86064 100644 --- a/src/biolink_model/datamodel/pydanticmodel_v2.py +++ b/src/biolink_model/datamodel/pydanticmodel_v2.py @@ -5382,6 +5382,9 @@ class EntityToPhenotypicFeatureAssociationMixin(EntityToFeatureOrDiseaseQualifie object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") has_count: Optional[int] = Field(None, description="""number of things with a particular property""") has_total: Optional[int] = Field(None, description="""total number of things in a particular reference set""") has_quotient: Optional[float] = Field(None) @@ -5420,6 +5423,9 @@ class PhenotypicFeatureToPhenotypicFeatureAssociation(PhenotypicFeatureToEntityA predicate: str = Field(..., description="""A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.""") object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -5722,7 +5728,7 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypicFeatureAssociationMixin, ChemicalToEntityAssociationMixin, Association): """ - This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect. + This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is a secondary undesirable effect. """ FDA_adverse_event_level: Optional[FDAIDAAdverseEventEnum] = Field(None) subject: str = Field(..., description="""the chemical entity or entity that is an interactor""") @@ -5872,6 +5878,9 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -5929,6 +5938,9 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -5991,6 +6003,9 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -6044,6 +6059,9 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -6101,6 +6119,9 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio object: str = Field(..., description="""behavioral feature that is the object of the association""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -6214,6 +6235,9 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -6266,6 +6290,9 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None, description="""Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).""") object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None, description="""Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") @@ -6322,6 +6349,9 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, Gene object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None, description="""Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -6376,6 +6406,9 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssoc object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None, description="""Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -6430,6 +6463,9 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityA object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None, description="""Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -6484,6 +6520,9 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None, description="""Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -6778,6 +6817,9 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -6939,6 +6981,9 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None, description="""Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") @@ -7270,6 +7315,9 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None, description="""Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).""") sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") disease_context_qualifier: Optional[str] = Field(None, description="""A context qualifier representing a disease or condition in which a relationship expressed in an association took place.""") + subject_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + object_specialization_qualifier: Optional[str] = Field(None, description="""A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.""") + anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml index c84cc8748..af3f3a5ba 100644 --- a/src/biolink_model/schema/biolink_model.yaml +++ b/src/biolink_model/schema/biolink_model.yaml @@ -1325,16 +1325,16 @@ slots: and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. examples: - - value: CHEBI:24431 + - value: CHEBI:5118 # fluoxetine description: >- In a MAXO annotation this would be a specialization in treatment of a disease. For example, fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term 'congenital myasthenic syndrome '4A.' - - value: CL:0000123 + - value: GO:0005634 # nucleus description: >- In an expression annotation this would be a specialization in location of an anatomical entity. For example, - "expression in the nucleas of hepatic cells" would be a specialization of "expression in hepatic cells" + "expression in the nucleus of hepatic cells" would be a specialization of "expression in hepatic cells" aspect qualifier: is_a: qualifier @@ -1461,12 +1461,15 @@ slots: - translator_minimal subject specialization qualifier: + is_a: specialization qualifier description: >- A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. - + in_subset: + - translator_minimal + range: uriorcurie subject form or variant qualifier: description: >- @@ -1534,6 +1537,17 @@ slots: in_subset: - translator_minimal + object specialization qualifier: + is_a: specialization qualifier + description: >- + A qualifier that composes with a core subject/object concept to define a more specific version of the + subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept + and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the + subject identifier. + in_subset: + - translator_minimal + range: uriorcurie + object form or variant qualifier: description: >- A qualifier that composes with a core subject/object concept to define a specific type, variant, @@ -9849,7 +9863,7 @@ classes: chemical or drug or treatment to disease or phenotypic feature association: description: >- This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature - where the disesae or phenotypic feature is a secondary undesirable effect. + where the disease or phenotypic feature is a secondary undesirable effect. is_a: association defining_slots: - subject @@ -10365,6 +10379,9 @@ classes: - object - sex qualifier - disease context qualifier + - subject specialization qualifier + - object specialization qualifier + - anatomical context qualifier defining_slots: - object slot_usage: diff --git a/src/biolink_model/scripts/classprefixes.py b/src/biolink_model/scripts/classprefixes.py index 575551fc1..fd0c23952 100644 --- a/src/biolink_model/scripts/classprefixes.py +++ b/src/biolink_model/scripts/classprefixes.py @@ -1,5 +1,5 @@ # Auto generated from class_prefixes.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-11-07T15:55:30 +# Generation date: 2024-11-07T16:12:28 # Schema: BiolinkClassPrefixes # # id: biolink-model-class-prefixes